# Issue with mne\_setup\_source\_space **URL:** \ **Category:** Mailing List Archive (read-only)\ **Tags:** list-archive\ **Created:** [March 3, 2014, 12:04pm UTC](https://mne.discourse.group/t/issue-with-mne-setup-source-space/681 "2014-03-03T12:04:29Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [March 3, 2014, 12:04pm UTC](https://mne.discourse.group/t/issue-with-mne-setup-source-space/681/1 "2014-03-03T12:04:29Z")
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](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 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, ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [March 3, 2014, 12:23pm UTC](https://mne.discourse.group/t/issue-with-mne-setup-source-space/681/2 "2014-03-03T12:23:45Z")
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](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](http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20140303/c1ffe38c/attachment.html) ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [March 3, 2014, 1:04pm UTC](https://mne.discourse.group/t/issue-with-mne-setup-source-space/681/3 "2014-03-03T13:04:17Z")
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, ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [March 3, 2014, 1:10pm UTC](https://mne.discourse.group/t/issue-with-mne-setup-source-space/681/4 "2014-03-03T13:10:52Z")
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 ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [March 3, 2014, 1:13pm UTC](https://mne.discourse.group/t/issue-with-mne-setup-source-space/681/5 "2014-03-03T13:13:51Z")
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, ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [March 3, 2014, 1:14pm UTC](https://mne.discourse.group/t/issue-with-mne-setup-source-space/681/6 "2014-03-03T13:14:58Z")
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](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 ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [March 3, 2014, 5:32pm UTC](https://mne.discourse.group/t/issue-with-mne-setup-source-space/681/7 "2014-03-03T17:32:17Z")
Hi, you can download a file from [http://kanboxshare.com/link/5EaoKFcEomfDbFE08KUg3xtk8ObG7FXLnFqHoFEzufBO9cD0YQnPjLRN9R4bsYsTuaqrRIDBSBEPT](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" \??? > 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](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 > > > [MyComplianceReport.com: Compliance and Ethics Reporting](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. > > \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ > Mne\_analysis mailing list > Mne\_analysis at nmr.mgh.harvard.edu > [Mne\_analysis Info Page](https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis) > > 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 > [MyComplianceReport.com: Compliance and Ethics Reporting](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/20140304/016bef38/attachment.html](http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20140304/016bef38/attachment.html) ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [March 3, 2014, 5:33pm UTC](https://mne.discourse.group/t/issue-with-mne-setup-source-space/681/8 "2014-03-03T17:33:33Z")
Thanks for the suggestion Lau. I will try it out tomorrow and revert back.