[Mne_analysis] mne make_scalp_surfaces error
Mads Jensen
mje.mads at gmail.com
Sun Oct 30 04:01:16 EDT 2016
Hi Leonardo,
Rather than installing libgfortran.so.1 you can also create a symbolic
link to the libgfortran.so.3 file that has worked for me in past.
If your are on a ubuntu based system the command is (from memory):
ln -s /usr/lib/x86_64-linux-gnu/libgfortran.so.3
/usr/lib/x86_64-linux-gnu/libgfortran.so.
- mads
On 30/10/16 01:36, Leonardo Barbosa wrote:
> Thank you for the feedback.
>
> I admit that the download page for the MNE-C is a bit confusing.
> On the top there is the old version 2.7.0, followed by the nightly-build
> 2.7.4, followed by the last stable version 2.7.3.
>
> I tried the 2.7.3, which I guess is the last stable version (from 2011),
> and got the same error.
>
> I installed the nightly-build (2016), and now it is working, although
> I'm not very comfortable running nightly-builds in production...
>
> Also, it complained about a missing library: libgfortran.so.1
>
> *mne_surf2bem: error while loading shared libraries: libgfortran.so.1:
> cannot open shared object file: No such file or directory*
>
> Which is weird, since it is an old lib, and I have libgfortran.so.3
> installed, and the previous MNE versions seemed to do just fine.
> I added an old libgfortran.so.1 available in the anaconda repository,
> but since I added the whole folder to the ld.so.conf, I'm getting some
> weird warnings...
> I think I'm going back to MNE-2.7.3-3268-Linux-x86_64 after I finish
> generating the surfaces, and remove libgfortran.so.1 from the path
>
> Is there a stable version of 2.7.4 ?
>
> Thank you,
> Leonardo
>
>
> 2016-10-28 14:29 GMT-05:00 Alexandre Gramfort
> <alexandre.gramfort at telecom-paristech.fr
> <mailto:alexandre.gramfort at telecom-paristech.fr>>:
>
> hi,
>
> your version of mne_surf2bem is too old.
>
> please try to install the latest version of mne C. Take the nightly
> build.
> The --force option was introduced much later than 2009.
>
> now I think we should fix this as mne_surf2bem should not be necessary
> for this operation.
>
> I opened an issue on github
>
> https://github.com/mne-tools/mne-python/issues/3709
> <https://github.com/mne-tools/mne-python/issues/3709>
>
> HTH
> Alex
>
>
> On Fri, Oct 28, 2016 at 1:09 AM, Leonardo Barbosa
> <lsbarbosa at gmail.com <mailto:lsbarbosa at gmail.com>> wrote:
> > Dear list,
> >
> > Since I changed to the the develop version (0.14.dev0), I've been
> seeing a
> > warning message whenever I try to do the co-registration using
> > mne.gui.coregistration:
> >
> > ------
> >
> > No high resolution head model was found for subject USER_2005_T1,
> using
> > standard head instead. In order to generate a high resolution head
> model,
> > run:
> >
> >
> > $ mne make_scalp_surfaces -s USER_2005_T1
> >
> >
> > ------
> >
> > https://drive.google.com/open?id=0B0p7WZ2wlTFSTjZQSGNMOHpCTGc
> <https://drive.google.com/open?id=0B0p7WZ2wlTFSTjZQSGNMOHpCTGc>
> >
> > So far, following the Head Model tutorial, I've been using
> >
> > mne watershed_bem -s USER
> > (output:
> https://drive.google.com/open?id=0B0p7WZ2wlTFSODIzekhIQ2tuNnM
> <https://drive.google.com/open?id=0B0p7WZ2wlTFSODIzekhIQ2tuNnM>)
> >
> > which generates the head surface .fif file in :
> >
> > bem/USER_2005_T1-head.fif (together with some other surface files)
> >
> > and did not have any further problems.
> >
> > Following the warning, I tried to run the
> >
> > mne make_scalp_surfaces -s USER_2005_T1
> >
> > and even though the high-resolution was created in
> >
> > bem/NCCAM_2005_T1-head-dense.fif (together with the surf/*seghead*
> files)
> >
> > I got the following error in the part that generates the medium
> tessellation
> > (output here :
> > https://drive.google.com/open?id=0B0p7WZ2wlTFSZHp0VVpBUWxNbXc
> <https://drive.google.com/open?id=0B0p7WZ2wlTFSZHp0VVpBUWxNbXc>).
> >
> > Therefore my question is: can I safely ignore the warning and use
> the lower
> > resolution bem generated by the watershed algorithm?
> > What would be the advantages of using the high-resolution version?
> >
> > One clear advantage for me it to use the high resolution when
> possible to
> > mark the fiducials, but I figure that for the actual forward model
> a lower
> > resolution must be used otherwise it would take long to compute all
> > electrical distances, no?
> >
> > Of note:
> >
> > * The same error occurs when I use the version 0.13-dev and 0.13
> stable.
> > * I'm using
> >
> > mne_surf2bem version 1.6 compiled at Dec 21 2009 19:47:09
> >
> > * I noticed that mne_surf2bem complains about a --force option, which
> > apparently do not exist.
> > If I try to remove the offending argument, I get a different error
> (output
> > here:
> https://drive.google.com/open?id=0B0p7WZ2wlTFSbHdTWkpub2N2T3c
> <https://drive.google.com/open?id=0B0p7WZ2wlTFSbHdTWkpub2N2T3c>)
> >
> > Any help is appreciated!
> >
> > Thank you,
> > Leonardo Barbosa
> >
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