Hi Alex,

That command just downloads the fs_install_mcr script into your freesurfer directory. These are two separate steps. Once downloaded, you can run

fs_install_mcr R2012b

as you would normally.

best

Andrew

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience" <ladn@email.gwu.edu>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Sunday, May 10, 2020 at 4:58 PM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Downloading Matlab runtime - ubuntu

        External Email - Use Caution        

Thank you Tim! 

Also I was wondering, how should I specify the version (i.e. R2012b) of matlab in the code -  "cd $FREESURFER_HOME/bin && curl https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_install_mcr -o fs_install_mcr && chmod +x fs_install_mcr" ?

All the best, 

Alex

On Sun, May 10, 2020 at 5:42 AM Tim Schäfer <ts+ml@rcmd.org> wrote:

        External Email - Use Caution       

You do not have write permission to $FREESURFER_HOME, which is /usr/local/freesurfer/ in your case, it seems. There are 2 options:

1) run the command again but put 'sudo ' in front. This should give you permission to write to that location.

2) install FreeSurfer into your user directory, where you have write access.

I would recommend option 1) if you have sudo access, especially if several users should be able to use the FreeSurfer installation.

Best,

Tim


> On May 10, 2020 at 8:02 AM "Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience" <ladn@email.gwu.edu> wrote:
>
>
>         External Email - Use Caution       
>
> Dear Freesurfer experts,
>
> I'm trying to download runtime for ubuntu using the instructions on the
> website and I'm struggling to resolve this error (seen below). Any ideas on
> how to fix this? Thank you and hope everyone is safe!
>
> cd $FREESURFER_HOME/bin && curl
> https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_install_mcr
> -o
> fs_install_mcr && chmod +x fs_install_mcr
>   % Total    % Received % Xferd  Average Speed   Time    Time     Time
>  Current
>                                  Dload  Upload   Total   Spent    Left
>  Speed
>   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--
>   0Warning: Failed to create the file fs_install_mcr: Permission denied
>  68  1988   68  1371    0     0   4436      0 --:--:-- --:--:-- --:--:--
>  4422
> curl: (23) Failed writing body (0 != 1371)
> alex@ubu19:/usr/local/freesurfer/bin$ fs_install_mcr R2012b
>   % Total    % Received % Xferd  Average Speed   Time    Time     Time
>  Current
>                                  Dload  Upload   Total   Spent    Left
>  Speed
> 100   177  100   177    0     0     77      0  0:00:02  0:00:02 --:--:--
>  77
> Archive:  installer.zip
>   End-of-central-directory signature not found.  Either this file is not
>   a zipfile, or it constitutes one disk of a multi-part archive.  In the
>   latter case the central directory and zipfile comment will be found on
>   the last disk(s) of this archive.
> unzip:  cannot find zipfile directory in one of installer.zip or
>         installer.zip.zip, and cannot find installer.zip.ZIP, period.
>
> Thank you,
> Alex Job Said
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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--
Tim Schäfer

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