questions

✉️ Mailing List Archive (read-only)
1

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?

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 )

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.

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

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.

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...

Are you using a noise covariance matrix?
What exact command did you use to generate it?
How does the time period you used to generate your noise covariance
relate to the time period you are trying to invert?
Did you make sure that --projon was used when generating your noise
covariance matrix?

2

Dan, see below, thanks,
-Jeff

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