[Mne_analysis] mne_analyze inverse display problem

[Jeff Eriksen]

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
>>>
>>>
>>>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