[Mne_analysis] Issue with mne_setup_source_space

[Matti Hamalainen]

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


-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20140303/c1ffe38c/attachment.html