[Mne_analysis] Issue with mne_setup_source_space

[Lau Møller Andersen]

Hi Kousik

It’’s probably related to your system setup. I had a similar problem.

Try the solution of Mads Jensen
https://github.com/mne-tools/mne-python/issues/774 i.e. creating a symbolic link to the right libgfortran
ln -s  /usr/lib/x86_64-linux-gnu/libgfortran.so.3  /usr/lib/x86_64-linux-gnu/libgfortran.so.1


Best

Lau
Den 03/03/2014 kl. 14.10 skrev Matti Hamalainen <msh at nmr.mgh.harvard.edu>:

> 
> Hello Kousik,
> 
> It should not matter where the MNE installation is. Do you mean by virtual drive that you are running MNE in a virtual machine? The "real" operating system might be missing libgfortran while the virtual machine has it. 
> 
> Let's see what others on this list say.
> 
> - Matti
> 
> On Mar 3, 2014, at 8:04 AM, kousik sarathy <sarathykousik at gmail.com> wrote:
> 
>> Hello Matti,
>> 
>> Thanks a ton. This worked. 
>> 
>> I got another problem where the shell was searching for 'libgfortran' shared library and could not find it. So I moved the whole installation 'into' the virtual drive and it now worked. Is that a relevant solution or does it have nothing to do with where the MNE is installed at all?
>> 
>> root at xubuntu-VirtualBox:~# mne_setup_source_space --ico -6
>> 
>> Setting up the source space with the following parameters:
>> 
>> SUBJECTS_DIR = /usr/local/freesurfer/subjects
>> Subject      = 014_NJO
>> Surface      = white
>> Octahedron subdivision grade 6
>> 
>> >>> 1. Creating the source space file /usr/local/freesurfer/subjects/014_NJO/bem/014_NJO-oct-6-src.fif...
>> mne_make_source_space: error while loading shared libraries: libgfortran.so.1: cannot open shared object file: No such file or directory
>> Source space creation failed
>> Temporary files removed.
>> 
>> 
>> Thanks,
>> 
>> --
>> Regards,
>> Kousik Sarathy, S
>> 
>> 
>> 
>> On Mon, Mar 3, 2014 at 1:23 PM, Matti Hamalainen <msh at nmr.mgh.harvard.edu> wrote:
>> 
>> Hello,
>> 
>> On Mar 3, 2014, at 7:04 AM, kousik sarathy <sarathykousik at gmail.com> wrote:
>> 
>>> Hello,
>>> 
>>> I am trying to create a mesh using MNE (following this tutorial: http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate). I am using the Xubuntu virutal box from FreeSurfer. I already carried out the steps in FreeSurfer successfully. 
>>> 
>>> I then followed the manual to setup MNE and here's what I did. Even then I get an error saying it cannot find a make_source file. 
>>> 
>>> Is there any solution someone could point out?
>>> 
>>> Here's the copy of my shell outputs.
>>> 
>>> root at xubuntu-VirtualBox:~# export MNE_ROOT=/media/sf_J_DRIVE/MNE-2.7.4-3436-Linux-i686
>>> root at xubuntu-VirtualBox:~# $MNE_ROOT/bin/mne_setup_sh
>> 
>> This should start with a dot
>> 
>> . $MNE_ROOT/bin/mne_setup_sh
>> 
>> 
>>> 
>>> MNE software location set to:    /media/sf_J_DRIVE/MNE-2.7.4-3436-Linux-i686
>>> MATLAB software not available
>>> 
>>> root at xubuntu-VirtualBox:~# $MNE_ROOT/bin/mne_setup
>>> 
>>> MNE software location set to:    /media/sf_J_DRIVE/MNE-2.7.4-3436-Linux-i686
>>> MATLAB software not available
>>> 
>>> root at xubuntu-VirtualBox:~# echo $SHELL
>>> /bin/bash
>>> root at xubuntu-VirtualBox:~# export SUBJECT=014_NJO
>>> root at xubuntu-VirtualBox:~# echo $SUBJECTS_DIR 
>>> /usr/local/freesurfer/subjects
>>> root at xubuntu-VirtualBox:~# cd $MNE_ROOT/bin
>> 
>> After correcting the step above, you do not need to go to the bin directory
>> 
>>> root at xubuntu-VirtualBox:/media/sf_J_DRIVE/MNE-2.7.4-3436-Linux-i686/bin# ./mne_setup_source_space --ico -6
>> 
>> The ./  can be removed, mne_setup_source_space works from anywhere
>> 
>>> 
>>> Setting up the source space with the following parameters:
>>> 
>>> SUBJECTS_DIR = /usr/local/freesurfer/subjects
>>> Subject      = 014_NJO
>>> Surface      = white
>>> Octahedron subdivision grade 6
>>> 
>>> >>> 1. Creating the source space file /usr/local/freesurfer/subjects/014_NJO/bem/014_NJO-oct-6-src.fif...
>>> ./mne_setup_source_space: 311: ./mne_setup_source_space: mne_make_source_space: not found
>>> Source space creation failed
>>> Temporary files removed.
>> 
>> This problem should be resolved after setting up MNE correctly, see above.
>> 
>> Best,
>> Matti
>> 
>> 
>> 
>> 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 Partners Compliance HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in error
>> but does not contain patient information, please contact the sender and properly
>> dispose of the e-mail.
>> 
>> 
> 
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> 
> 
> 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 Partners Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in error
> but does not contain patient information, please contact the sender and properly
> dispose of the e-mail.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20140303/bc7cc4ed/attachment.html