[Mne_analysis] Issue with mne_setup_source_space

kousik sarathy sarathykousik at gmail.com
Mon Mar 3 08:04:17 EST 2014
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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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