[Mne_analysis] mne_analyze inverse display problem

[Jeff Eriksen]

I did not get any response on the issue below, which prevents me from viewing my inverse results. Anyone have any suggestions? I can post my files if necessary. Thanks,
-Jeff

From: Jeff Eriksen <eriksenj at ohsu.edu<mailto:eriksenj at ohsu.edu>>
To: Matti Hamalainen <msh at nmr.mgh.harvard.edu<mailto:msh at nmr.mgh.harvard.edu>>
Cc: "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: noise covariance calculation

Hi Matti,

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. 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?

-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>>
Subject: Re: noise covariance calculation


What's the problem exactly?

As an alternative, you can mark it bad.

- Matti

On Jun 11, 2012, at 6:57 AM, Jeff Eriksen wrote:

OK, but I am having trouble leaving it out. I tried what you suggested April 20:

***************************************************************************************************
Jeff,

This is because the data file contains the reference electrode as the 257th electrode and does not get a location assinged with the --nonames option. We need to fake a little bit to make the reference to "disappear" since we do not need it.
Fortunately, there is an easy solution:

1. Create a text file (eg, VREF.rename) with a line

VREF:VREF:502

2. Say

 mne_rename_channels --fif A1_smpl.fif --alias VREF.rename

This will make the VREF channel a 'MISC' channel and it will not cause trouble again in the forward calculation.
***************************************************************************************************
But the console output indicated nothing was removed. I then tried to modify my gsn257.elp to gsn256.elp, as follows:

3 2
1
%N gsn256.elp
4 256
%F 0.00000e+00 1.05638e-01 -2.05108e-02
%F -7.82694e-02 4.53860e-03 -3.76056e-02
%F 7.82694e-02 4.53860e-03 -3.76056e-02
%S 400
%N E1
%N 6.96223e-02 5.38242e-02 -2.19061e-02
%S 400
%N E2
…
%S 400
%N E256
%N -6.86103e-02 -1.41550e-03 -9.14913e-02
%S 502
%N Ref
%N 0.00000e+00 0.00000e+00 9.68308e-02

But again no luck. Console output says:

Read a total of 260 digitization points. 257 electrode labels present
Transformed LPA :  -78.3    0.0    0.0 mm
Transformed NAS :    0.0  102.5   -0.0 mm
Transformed RPA :   78.3    0.0    0.0 mm
Transformed 260 locations to the MNE head coordinate frame.
No reference electrode location present
257 EEG electrode locations assigned

The EGI software insists on exporting the reference channel, so it is always present in the EDF file it creates. Can you soggest any other way to ignore it, and not include it in the average or other processing?
Thanks,

-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>>
Subject: Re: noise covariance calculation


On Jun 11, 2012, at 5:37 AM, Jeff Eriksen wrote:

Matti,

I was trying to include the zero-value VREF channel (Cz) since knowing its physical location provides a small amount of spatial information. Looks like it is better for me to just leave it out. I will remove channel 257 completely and re-run whatever is necessary and let you know. Thanks,

Jeff,

You must leave it out, there is no option.

- Matti




---------

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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