[Mne_analysis] Issue with mne_setup_source_space

[Matti Hamalainen]

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.
> 
> 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20140303/420867a5/attachment.html