[Mne_analysis] mne make_scalp_surfaces error

[Leonardo Barbosa]

Cool, the symbolic link did the trick (thanks mads!).

I'm able to run "mne make_scalp_surfaces" without further issues.
Also the co-registration looks good.

Thank you for all the feedback!,

Leonardo

2016-10-30 3:51 GMT-05:00 Alexandre Gramfort <
alexandre.gramfort at telecom-paristech.fr>:

> hi,
>
> > Also, it complained about a missing library:  libgfortran.so.1
>
> yes we know :(
>
> you can use mads trick
>
> here is also the lib you may need on linux:
>
> https://dl.dropboxusercontent.com/u/2140486/libgfortran.so.1.i686.zip
> https://dl.dropboxusercontent.com/u/2140486/libgfortran.so.1.x86_64.zip
>
> don't trouble yourself about using a nightly version the MNE-C code. It
> is a very stable. The code changes are much less frequent than with
> mne-python.
>
> Sorry for all this hassle.
>
> Best,
> Alex
>
>
> > 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>:
> >>
> >> 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
> >>
> >> HTH
> >> Alex
> >>
> >>
> >> On Fri, Oct 28, 2016 at 1:09 AM, Leonardo Barbosa <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
> >> >
> >> > So far, following the Head Model tutorial, I've been using
> >> >
> >> > mne watershed_bem -s USER
> >> > (output: 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).
> >> >
> >> > 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)
> >> >
> >> > Any help is appreciated!
> >> >
> >> > Thank you,
> >> > Leonardo Barbosa
> >> >
> >> > _______________________________________________
> >> > Mne_analysis mailing list
> >> > Mne_analysis at nmr.mgh.harvard.edu
> >> > 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
> >> > 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
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >
> >
> >
> > _______________________________________________
> > Mne_analysis mailing list
> > Mne_analysis at nmr.mgh.harvard.edu
> > 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
> > 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
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20161031/fe318d68/attachment.html