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Hello Ben,

For packages to install, see the following wiki page,

https://surfer.nmr.mgh.harvard.edu/fswiki/BuildRequirements

Usually to expand the freesurfer *.tar.gz archive under /usr/local, you would need sudo/root privileges, e.g.

$ cd /usr/local
$ sudo tar zxpf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz
….
.. output deleted

- and you would end up with /usr/local/freesurfer and in turn do

$ export FREESURFER_HOME=/usr/local/freesurfer

But if you don’t have sudo privileges, e.g., it does not work to do
$ sudo touch /usr/local/foo
$ sudo rm /usr/local/foo

- then you may want to consider putting freesurfer under your $HOME directory or somewhere you have permission to write files w/o needing to use sudo, e.g.,

$ cd $HOME
$ tar zxpf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz
$ export FREESURFER_HOME=$HOME

- R.


On Mar 3, 2020, at 12:53, Benjamin Ineichen <bv.ineichen@gmail.com> wrote:

        External Email - Use Caution        


Dear Freesurfer experts,

Even though this problem has been raised in the archives, I was not able to find a specific solution to my problem.

I installed Freesurfer on a virtual machine which runs Ubuntu 18.04.4 (Host system: Windows 10). But it seems that Freesurfer is not installed properly. Upon running the installation test, I get the following errors:

1.) command line: cp $FREESURFER_HOME/subjects/sample-001.mgz .
Error: cp: cannot create regular file './sample-001.mgz': Permission denied

2.) command line: mri_convert sample-001.mgz sample-001.nii.gz
Error: mri_convert.bin sample-001.mgz sample-001.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 reuter Exp $
reading from sample-001.mgz...
mghRead(/usr/local/sample-001.mgz, -1): could not open file

3.) command line: freeview
Error: freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory.

My permissions are: drwxrwsr-x for freesurfer.

Any advice?

Many thanks!

/Ben



-- 
____________________________________
Benjamin Victor Ineichen, MD PhD
Karolinska Institutet
Center for Molecular Medicine
Stockholm, Sweden
+41 76 391 04 01

Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen
Karolinska Institutet
Center for Molecular Medicine
Stockholm, Sweden
+41 76 391 04 01
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