Dipole fitting problem

✉️ Mailing List Archive (read-only)
1

Hello Folks!
I ran into this problem when trying to calculate dipoles:
When setting up , this message appears:

"All desire channels not found in the covariance matrix" (see attachment for an example). And of course it can't calculate the dipole.
Do you know what the problem is?

I would really appreciate if you could give me some advice!

Thank you very much,

Katica
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2

It looks like CP2 is missing from the covariance matrix file. Did you
remove or rename channels before or after calculating the covariance
matrix?

D

3

Hi D!
Thanks for your fast response
So I did do rename alias for none EEG channels (not CP2) and also marked bad channels, but CP2 is not one of them. I did this before calculating the default noise covariance matrix.

Any thoughs on how I can fix this?
Thanks!!

Katica

4

Hi Katica,

In order to help us help you:
Please send us the exact lines you ran in mne_process_raw etc. (in
order) with each command on separate lines. throughout the whole
processing stream. Along with the raw text file you used with
mne_rename_channels. Also, please include what system this data is
recorded from.

Thanks,
D

5

Hi D!
I am rookie at all this, so hopefully what I am sending is ok. If not, please let me know!
Also, I am not sure what you mean with "what system this data is recorded from". We get our EEG and MRI from MGH databases.

Thank you very much!
Katica

6

Hi Katica,

Did you run mne_process raw? How did you create the average and
covariance matrix files?

7

Ok, so how do they get created? You are creating the average and the
covariance matrix files? I can see from one of the files there is an
average file:

2 bad channels read from
/home/spaz/Cat/subjects/PtMGH012/EEG/MGH012_clip2_onsetaverage.fif:
CZ CPZ
Loaded dataset 06/13/13 08:47:06>Average to trigger # 1002>average
from /home/spaz/Cat/subjects/PtMGH012/EEG/MGH012_clip2_onsetaverage.fif
Loaded all requested data from
/home/spaz/Cat/subjects/PtMGH012/EEG/MGH012_clip2_onsetaverage.fif

Also can you send me the output of your mne_inverse_operator command?
I am not familiar with this --eegnoise option, and I am not sure where
it comes from.

Thanks,
D

8

I think we don't!

The average files you see are spikes averages.

attached is the inv operator output

Thanks again!
K

9

Hi Katica,

It may be easier if you can zip up a folder with the data and upload
it for us to look at ( https://gate.nmr.mgh.harvard.edu/filedrop2/ ).
You can send the link to dwakeman at nmr.mgh.harvard.edu . Can you tell
me how you created the spike average file?

Thank You,
Dan

10

This was solved off list. It turned out to be different channels were
marked bad and thus the same inverse operator couldn't be used.