[Mne_analysis] mne_analyze inverse display problem

Thu Jun 28 20:02:11 EDT 2012

Matti and Eric,

I have it working now. I was modifying my local bash profile, but out sysadmin told me to not do that as the "master" profile was doing things correctly. Good suggestion on Eric's part to try FreeSurfer by itself.

-Jeff

From: Matti Hamalainen <msh at nmr.mgh.harvard.edu<mailto:msh at nmr.mgh.harvard.edu>>
To: Jeff Eriksen <eriksenj at ohsu.edu<mailto:eriksenj at ohsu.edu>>
Cc: Eric Larson <larson.eric.d at gmail.com<mailto:larson.eric.d at gmail.com>>, "mne_analysis at nmr.mgh.harvard.edu<mailto:mne_analysis at nmr.mgh.harvard.edu>" <mne_analysis at nmr.mgh.harvard.edu<mailto:mne_analysis at nmr.mgh.harvard.edu>>
Subject: Re: [Mne_analysis] mne_analyze inverse display problem

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<mailto: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<mailto: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<mailto: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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---------

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

msh at nmr.mgh.harvard.edu<mailto:msh at nmr.mgh.harvard.edu>
mhamalainen at partners.org<mailto:mhamalainen at partners.org>

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