[Mne_analysis] questions

Jeff Eriksen eriksenj at ohsu.edu
Mon Jun 11 18:18:50 EDT 2012
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Dan, see below, thanks,
-Jeff

On 6/11/12 2:13 PM, "dgw" <dgwakeman at gmail.com> wrote:

>Hi Jeff,
>
>We are getting closer. Please make sure to send your emails to the list
>so that everyone can learn (and help)
>
>
>
>Dan G. Wakeman wrote:
>> 
>> 
>> Hi Matti,
>> 
>> I followed your instructions as follows:
>> 
>> Changed time scales to 4-253 ms to avoid flat segments at begin and end
>> of EEG
>> Had already done 1-100 Hz bandpass filtering
>> Marked VREF as bad
>> Recalculated everything except electrode alignment
>Does this mean you recalculated the noise covariance matrix and inverse
>solution?
Yes

>> Loaded average and surfaces back into mne_analyze
>> 
>> When viewing inverse results on the inflated surface, they do not look
>> any different than before, that is:
>> a. Source activations do not generally match scalp EEG
>> b. For dSPM and sLORETA, most source activity is confined to R hemi
>> 
>> Questions:
>> 1. It looks like I can examine the noise-cov matrix with Matlab ­ what
>> should I see, good or bad?
>There are some examples (particularly on the webpage www.martinos.org/mne
>)
I will look at these, but as I dug into the Matlab script mne_read_cov, I
found unknown items such as "node" and "kind", and looking deeper at the
fif routines I did not yet find enough info to be able to set these.

>> 2. Alex G suggested I use ico5, not ico3. Other than higher spatial
>> resolution, that should not be cuasing the problems I see (?)
>Well, it is theoretically possible. ico 3 is very bad for any
>orientation constraints (which i believe you indicated you were using in
>an earlier e-mail). It is ok, to user for loose/no orientation
>constraint, although very misleading. I would never recommend using
>anything less than ico 5, and even with ico 5 I recommend using the
>loose variable orientation constraints.
I agree I should not have used fixed orientation with ico3, did not think
that through. I will try ico5 and loose orientation

>> 3. Alex also suggested I use a diagonal noise-cov matrix ­ how would I
>> go about that? If I knew what to put in it, I suppose I could create
>>and 
>> save using Matlab toolbox
>there is the --diagnoise option in mne_do_inverse_operator
Thanks, I will try that as well

>> 4. Is there any way to confirm that channel 257 has indeed been
>> eliminated in the averaging and covariance calculation?
>Well, did you check the output when re-running the commands. Did it talk
>about the bad channels detected? It is also possible to check with the
>MATLAB toolbox.
I did not always check, will look in more detail next time

>> 5. To that end, I have not been able to view the average EEG ­ the
>> window is blank. Someone suggested I create a new layout, but why can't
>> the software see the layouts I already created for the raw EEG?
>It should be able to see them, if you put them in the right directory as
>described in the manual. You should be able to select it using Adjust ->
>Select trace layout...
If I can get to them when viewing raw data, I would think they are in the
right directory...
But I will re-check

>
>Are you using a noise covariance matrix?
yes
>What exact command did you use to generate it?
I did it in mne_browse_raw
>How does the time period you used to generate your noise covariance
>relate to the time period you are trying to invert?
Same time periods - full 255 seconds
>Did you make sure that --projon was used when generating your noise
>covariance matrix?
Matti said it was irrelevant as the only projection I would be using is
the average ref for EEG

>
>> 6. I do not understand how to set the eegflat value - what should by
>> entered?
Any suggestion here?
-Jeff

>> 
>> 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>>
>> Cc: Dan G Wakeman <dwakeman at nmr.mgh.harvard.edu
>> <mailto:dwakeman at nmr.mgh.harvard.edu>>
>> Subject: Re: noise covariance calculation
>> 
>> 
>> On Jun 1, 2012, at 3:49 AM, Jeff Eriksen wrote:
>> 
>>> Matti,
>>>
>>> Here is my difficulty. I think I need to do something like this:
>>>
>>> mne_process_raw
>>> --raw A6_ec1_fen_ds250_raw.fif
>>> --projon
>>> --savecovtag -cov
>>> ­cov A1_ec1_fen_ds250.cov
>>>
>>> But I do not have the last .cov file. The only example I have to go on
>>> it the audvis.cov supplied with the sample subject, but I cannot
>>> figure out how I would modify it to work with my continuous raw files.
>>>
>>> I believe I did manage to calculate the noise-cov for my first
>>> subject, but the .cov file I have for that subject is not a text file,
>>> and I have no idea now where it came from.
>>>
>>> Also, in the above, do I really need the ‹projon switch? I am not
>>> clear if that is needed to enforce the average reference for EEG data.
>> 
>> 
>> Jeff,
>> 
>> It looks like you figured out how to compute the covariance. Here are a
>> few points:
>> 
>> 1. Change the time scale in both in your ave and cov files to go from,
>> e.g., 4 to 253 seconds because there are zeros in the beginning and end
>> of your raw data file.
>> 2. I propose you use a highpass filter, e.g., at 0.5 Hz to get rid of
>> the dc offsets.
>> 2. The last channel (VREF) in your data file is flat and it messes up
>> the estimates.  Mark it bad:
>> 
>> * Create a file called, e.g., VREF.bad which contains one line: VREF
>> * mne_mark_bad_channels --bad VREF.bad A6_ec1_fen_ds250_raw.fif
>> * This produces the output
>> 
>> mne_mark_bad_channels version 1.1 compiled at Jun  4 2012 05:32:20
>> 
>> Read bad channel list from: VREF.bad
>> 
>> 1 bad channels from VREF.bad:
>>         <VREF> 
>> 
>> A6_ec1_fen_ds250_raw.fif ... [done]
>> 
>> * You can also mark bad channels interactively, see Manual sections
>> 11.4.1 and 4.9.
>> * Recreate both the 'average' and the 'noise covariance'
>> * Recreate the inverse operator
>> 
>> 3. You can specify either --projon or --projoff swich (after marking
>> VREF bad). The source estimates are always calculated with the average
>> reference on. 
>> 
>> After eliminating VREF and recalculating the noise covariance and the
>> inverse operator, you source estimates should be more reasonable.
>> 
>> - 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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>





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