[Mne_analysis] Dipole fitting problem
dgw
dgwakeman at gmail.com
Fri Mar 14 16:16:16 EDT 2014
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.
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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