Issue with mne_setup_source_space

system · March 3, 2014, 12:04pm

Hello,

I am trying to create a mesh using MNE (following this tutorial:
Source reconstruction of event-related fields using minimum-norm estimation - FieldTrip toolbox). 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

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
root at xubuntu-VirtualBox:/media/sf_J_DRIVE/MNE-2.7.4-3436-Linux-i686/bin#
./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_setup_source_space: 311: ./mne_setup_source_space:
mne_make_source_space: not found
Source space creation failed
Temporary files removed.

Thanks,

system · March 3, 2014, 12:23pm

Hello,

Hello,

I am trying to create a mesh using MNE (following this tutorial: Source reconstruction of event-related fields using minimum-norm estimation - FieldTrip toolbox). 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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system · March 3, 2014, 1:04pm

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,

system · March 3, 2014, 1:10pm

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

system · March 3, 2014, 1:13pm

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,

system · March 3, 2014, 1:14pm

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

system · March 3, 2014, 5:32pm

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 ??9:14? "kousik sarathy" <sarathykousik at gmail.com>???

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

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

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

Hello,

Hello,

I am trying to create a mesh using MNE (following this tutorial:
Source reconstruction of event-related fields using minimum-norm estimation - FieldTrip toolbox). 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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system · March 3, 2014, 5:33pm

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

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