[Mne_analysis] Issue with mne_setup_source_space

[kousik sarathy]

Thanks for the suggestion Lau. I will try it out tomorrow and revert back.

--
Regards,
Kousik Sarathy, S



On Mon, Mar 3, 2014 at 2:14 PM, Lau Møller Andersen <lau.andersen at cnru.dk>wrote:

> 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
>>
>>
>>
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