[Mne_analysis] mne make_scalp_surfaces error

[Alexandre Gramfort]

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
>> >
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