[Mne_analysis] Issue with mne_setup_source_space

[thismoment]

Hi,

you can download a file from
http://kanboxshare.com/link/5EaoKFcEomfDbFE08KUg3xtk8ObG7FXLnFqHoFEzufBO9cD0YQnPjLRN9R4bsYsTuaqrRIDBSBEPT
and change name into desired one.

It worked when I encountered the same problem.

Junpeng Zhang
2014-3-3 下午9:14于 "kousik sarathy" <sarathykousik at gmail.com>写道：

> Yes. I meant Virtual machine. It's actually the FreeSurfer virtual machine
> that I use for MNE too.
>
> Okay. But as of now the problem seems fixed.
>
> Thank you,
>
>
> --
> Regards,
> Kousik Sarathy, S
>
>
>
> On Mon, Mar 3, 2014 at 2:10 PM, Matti Hamalainen <msh at nmr.mgh.harvard.edu>wrote:
>
>>
>> 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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>>
>>
>>
>
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