[Mne_analysis] Dipole fitting problem

[dgw]

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

On Fri, Mar 14, 2014 at 1:22 PM, Boric, Katica A.
<KBORIC at mgh.harvard.edu> wrote:
> I think we don't!
>
> The average files you see are spikes averages.
>
> attached is the inv operator output
>
> Thanks again!
> K
>
>
>
>
>
> ________________________________________
> From: dgw [dgwakeman at gmail.com]
> Sent: Friday, March 14, 2014 12:54 PM
> To: Boric, Katica A.; mne_analysis at nmr.mgh.harvard.edu
> Subject: Re: [Mne_analysis] Dipole fitting problem
>
> 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
>
> On Fri, Mar 14, 2014 at 12:42 PM, Boric, Katica A.
> <KBORIC at mgh.harvard.edu> wrote:
>> Hi D!
>> We don't do that (what we do is on the file that says commands) And actually we do not create the average and covariance matrix files...
>> ________________________________________
>> From: dgw [dgwakeman at gmail.com]
>> Sent: Friday, March 14, 2014 12:37 PM
>> To: Boric, Katica A.
>> Cc: mne_analysis at nmr.mgh.harvard.edu
>> Subject: Re: [Mne_analysis] Dipole fitting problem
>>
>> Hi Katica,
>>
>> Did you run mne_process raw? How did you create the average and
>> covariance matrix files?
>>
>> On Fri, Mar 14, 2014 at 12:26 PM, Boric, Katica A.
>> <KBORIC at mgh.harvard.edu> wrote:
>>> 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
>>> ________________________________________
>>> From: dgw [dgwakeman at gmail.com]
>>> Sent: Friday, March 14, 2014 11:45 AM
>>> To: Boric, Katica A.
>>> Cc: mne_analysis at nmr.mgh.harvard.edu
>>> Subject: Re: [Mne_analysis] Dipole fitting problem
>>>
>>> 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
>>>
>>> On Fri, Mar 14, 2014 at 11:34 AM, Boric, Katica A.
>>> <KBORIC at mgh.harvard.edu> wrote:
>>>> 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
>>>> ________________________________________
>>>> From: mne_analysis-bounces at nmr.mgh.harvard.edu [mne_analysis-bounces at nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman at gmail.com]
>>>> Sent: Friday, March 14, 2014 11:03 AM
>>>> To: Boric, Katica A.
>>>> Cc: mne_analysis at nmr.mgh.harvard.edu
>>>> Subject: Re: [Mne_analysis] Dipole fitting problem
>>>>
>>>> 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
>>>>
>>>> On Fri, Mar 14, 2014 at 10:58 AM, Boric, Katica A.
>>>> <KBORIC at mgh.harvard.edu> wrote:
>>>>>
>>>>> 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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