[Mne_analysis] mne_analyze inverse display problem

[Matti Hamalainen]

Jeff,

The subject name is coded into the source space, forward solution, and inverse operator files. This means that the directory structure under SUBJECTS_DIR has to remain intact. Otherwise, the location does not matter as long as SUBJECTS_DIR is set correctly. HOWEVER, if you have used media with a windows file system on it to transfer files, strange things may happen because symbolic links are not supported. 

- Matti

On Jun 28, 2012, at 3:49 AM, Jeff Eriksen 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
>>>> 
>>>> 
>>>> 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
> 
> 

---------

Matti Hamalainen, Ph.D.
Athinoula A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital

msh at nmr.mgh.harvard.edu
mhamalainen at partners.org






-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20120628/6a5a9883/attachment.html