[Mne_analysis] mne_analyze inverse display problem

[Eric Larson]

That's odd---going between machines should work. I've done
parcellation and source space/BEM setup on one Linux machine, moved
the subject structural to a different linux machine with a different
directory structure, and after generating averages and inverses there,
copied everything to my OSX install (again with a different path
structure) where they load without issue.

On both my OSX and Linux installs, the variables I set are
MATLAB_ROOT, SUBJECTS_DIR, and SUBJECT, then run
$MNE_ROOT/bin/mne_setup_sh and $FREESURFER_HOME/SetUpFreeSurfer.sh. I
assume you've done this, but if you have Freesurfer installed, you can
double-check that SUBJECTS_DIR and such are set appropriately by doing
"tkmedit SUBJNAME T1" where SUBJNAME is the name of your subject will
also test to see if that subject's structural is in the expected
location. You can also then try loading the surfaces that MNE looks
for

It's important to note, however, that the Freesurfer folks (and maybe
MNE, too?) recommend against switching versions mid-analysis. If it's
not too difficult, I'd recommend re-running the analysis on Linux.
Might be the easiest solution in any case.

Eric

On Wed, Jun 27, 2012 at 5:49 PM, Jeff Eriksen <eriksenj at ohsu.edu> wrote:
> Eric et al.,
>
> I moved my files from Mac to Linux. I can open the averaged EEG, but when
> I try to open the surfaces they cannot be found. I am sure this is because
> their location was hard-coded in the fif files. Is there any way to change
> this? Otherwise I seem to have two options.
>
> Set up identical directory structure on Linux to match Mac folders
> Or
> Re-run the part of the MNE analysis that code the locations of surface
> (and other?) files into the fif files.
>
> I have set the appropriate FreeSurfer environmental variables, thinking
> that would be enough, but apparently not.
>
> Thanks,
> -Jeff
>
> On 6/27/12 10:51 AM, "Eric Larson" <larson.eric.d at gmail.com> wrote:
>
>>Are you using OSX? I've had an issue with the display not working
>>appropriately sometimes (alternates between blank/maybe white and some
>>fixed image even when it should be updating). I chalked it up to an
>>improper implementation of OpenGL/XWindows on OSX since I have never
>>run into the same issue on linux x86_64 or i686.
>>
>>Eric
>>
>>
>>On Wed, Jun 27, 2012 at 10:47 AM, Jeff Eriksen <eriksenj at ohsu.edu> wrote:
>>> Alex,
>>>
>>> I did mark the VREF channel as bad.
>>>
>>> I used the --diagnoise switch so as not to have to worry about the
>>> actually noise-cov matrix at this point.
>>>
>>> The problem is not a scaling issue - it is a severe display issue/bug -
>>> the entire pane goes completely white, no surface displayed, nothing,
>>>and
>>> at that point I can not even get back to any of the three types of
>>> inverses. The only way to continue is to exit mne_analyse and restart
>>>it.
>>>
>>> Thanks,
>>> -Jeff
>>>
>>> On 6/26/12 11:50 PM, "Alexandre Gramfort" <gramfort at nmr.mgh.harvard.edu>
>>> wrote:
>>>
>>>>hi,
>>>>
>>>>> I tried ico-4 and ico-5, and still get the same results ­ poor
>>>>>correlation
>>>>> between scalp and cortical sources. I have not tried the ‹loose option
>>>>>yet,
>>>>> will do that this afternoon. I did try ‹diagnoise, and that seemed to
>>>>> improve matters (though I do not know why ­ the manual says most users
>>>>>never
>>>>> need to use this), but I am experiencing issues with mne_analyse in
>>>>>trying
>>>>> to display the three different estimates.
>>>>
>>>>did you correct for the bad channel like matti suggested? did you take a
>>>>look
>>>>at the noise covariance you estimated from the data? Ideally it should
>>>>be
>>>>as diagonal as possible with similar values along the diagonal. See e.g.
>>>>
>>>>http://martinos.org/mne/auto_examples/plot_estimate_covariance_matrix_ra
>>>>w.
>>>>html
>>>>
>>>>for an example of noise covariance plot.
>>>>
>>>>> As I change from dSPM, which comes
>>>>> up as defult, to MNE, the inflated brain pane goes white, and I cannot
>>>>>get
>>>>> it back until I exit and go back in. Ever seen this before?
>>>>
>>>>you certainly need to adjust the scaling of the colorbar.
>>>>
>>>>do you see something like this:
>>>>
>>>>http://martinos.org/mne/_images/MNE_preferences.png
>>>>
>>>>taken from :
>>>>http://martinos.org/mne/manual/analyze.html#ch-interactive-analysis
>>>>
>>>>Alex
>>>>
>>>>
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