[Mne_analysis] mne_compute_raw_inverse gave perfectly correlated source current estimates

[Matti Hamalainen]

On Feb 23, 2012, at 9:20 AM, Kai Hwang wrote:

> Hi Matti and Alex,
> Yes MEG-only solution worked. Now source estimates are no longer
> perfectly correlated. Any idea what went wrong regarding including EEG
> data into the inverse solution?
> 
> I used labels created by freesurfer's a2009 parcelation, I double
> checked and they are correct.

Are some of the EEG channels dysfunctional and not marked bad? Have you checked the EEG data by switching the average EEG reference off in mne_browse_raw?

- Matti


> 
> Thanks!
> Kai
> 
> 
> On Thu, Feb 23, 2012 at 8:04 AM, Matti Hamalainen
> <msh at nmr.mgh.harvard.edu> wrote:
>> 
>> Hi Kai,
>> 
>> In this kind of a case I suspect something is wrong with the noise covariance. What happens if you do an MEG-only solution, i.e., omit the --eeg option from mne_do_inverse_operator?
>> 
>> - Matti
>> 
>> 
>> On Feb 23, 2012, at 8:02 AM, Kai Hwang wrote:
>> 
>>> Hi Alex, I changed --nave to 100 and still got perfect correlations.
>>> Actually source estimates look identical between --nave 1 and --nave
>>> 100.
>>> Any other suggestions?
>>> Thanks
>>> Kai
>>> 
>>> On Thu, Feb 23, 2012 at 2:44 AM, Alexandre Gramfort
>>> <gramfort at nmr.mgh.harvard.edu> wrote:
>>>> Hello Kai,
>>>> 
>>>> a possible explanation is the "nave" used to set the regularization of
>>>> the inverse problem.
>>>> 
>>>> if you work with raw data, nave is 1 while with 100 epochs averaged
>>>> it's 100 and the inverse
>>>> solution is then far less regularized. A solution is to set the --nave
>>>> option to a higher value in
>>>> mne_compute_raw_inverse but you might amplify noise.
>>>> 
>>>> hope this helps
>>>> 
>>>> Alex
>>>> 
>>>> On Thu, Feb 23, 2012 at 3:02 AM, Kai Hwang <kai.hwang at gmail.com> wrote:
>>>>> Hello,
>>>>> 
>>>>> I am trying to use mne_compute_raw_inverse to project single trial
>>>>> epochs onto the surface. The command finishes without erros, but is
>>>>> generating perfectly correlated source estimates from distant regions.
>>>>> The scale and sign of current estimates differ, but the correlation is
>>>>> either 1 or -1.
>>>>> Below is the command:
>>>>> 
>>>>> #do forward solution
>>>>> mne_do_forward_solution --overwrite \
>>>>> --meas ${s}_prep_ave.fif --subject ${s} --fwd ${s}_prep_ave_fwd.fif --meg --eeg
>>>>> 
>>>>> #create inverse operator
>>>>> mne_do_inverse_operator --fwd ${s}_prep_ave_fwd.fif --depth \
>>>>> --loose 0.2 --meg --eeg --senscov ${s}_prep_cov.fif --subject ${s}
>>>>> 
>>>>> #project raw data, for each label
>>>>> mne_compute_raw_inverse --in ${s}_${rn}_sss_ds_raw.fif \
>>>>> --inv ${s}_prep_ave_fwd.fif-meg-eeg-inv.fif \
>>>>> --picknormalcomp \
>>>>> --align_z \
>>>>> --labeldir ./ALL-Labels \
>>>>> --orignames \
>>>>> --out ${s}-{rn}-label-source
>>>>> 
>>>>> However, the same inverse operator worked fine with averaged evoked
>>>>> data, results are reasonable when viewed in mne_analyze.
>>>>> Any idea what could have gone wrong?
>>>>> 
>>>>> Thanks!
>>>>> Kai
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>> 
> 
> 
> 
> -- 
> Kai Hwang, M.A.
> Laboratory of Neurocognitive Development
> Western Psychiatric Institute and Clinic
> University of Pittsburgh Medical Center
> http://www.pitt.edu/~kah124/
> 
>