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
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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 =$FREESURFER_HOME./fs_install_mcr R2019b sudo: FREESURFER_HOME: command not found
The same problem persists yet again :( Does the problem lie somewhere else?
Sincerely, Justina
On Tue, Sep 13, 2022 at 8:49 PM Wighton, Paul <PWIGHTON@mgh.harvard.edumailto:PWIGHTON@mgh.harvard.edu> wrote: Ah ok, let's try this:
cd /usr/local/freesurfer/7.3.2/bin sudo FREESURFER_HOME=$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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Justina Lee <justinalee56@gmail.commailto:justinalee56@gmail.com> Sent: Tuesday, September 13, 2022 2:37 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found
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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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Justina Lee <justinalee56@gmail.commailto:justinalee56@gmail.com> Sent: Tuesday, September 13, 2022 2:28 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found
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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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Justina Lee <justinalee56@gmail.commailto:justinalee56@gmail.com> Sent: Tuesday, September 13, 2022 1:58 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found
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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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of You Na Lee <justinalee56@gmail.commailto:justinalee56@gmail.com> Sent: Tuesday, September 13, 2022 9:01 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto: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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