[Mne_analysis] mne_analyze inverse display problem

[Jeff Eriksen]

Eric,

I may no be doing the mne_setup_sh part, will check on that tomorrow. With
all you have given me, I can now probably figure it out. I have not done
any real analysis yet, just learning the ropes. Thanks,

-Jeff

On 6/27/12 6:44 PM, "Eric Larson" <larson.eric.d at gmail.com> wrote:

>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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>>>>
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