[Mne_analysis] Do I need to setup mri and do watershed etc procedure every time I re-analyze the data

[Hari Bharadwaj]

Hi,
  I wouldn't get a chance to go through your scripts but I'm attempting to
answer just the last question about #trials:

MNE is only weakly affected by the #trials especially when you have a
larger #trials to start with since it enters the calculation only as a
weighting between data fit and the prior (the norm penalty). Ultimately it
is in units of real current (nA).

dSPM and sLORETA on the other hand normalize the MNE further by the
estimated source noise variance and since that goes down with increase in
#trials, one would expect the dSPM and sLORETA to sort of go up
proportional to sqrt(N) where N = #trials.

If the estimate of the noise covariance has converged and good (i.e large
degree of freedom), then I personally don't have a particular preferance
for MNE or dSPM when it comes to group level averaging since MNE is nA and
dSPM/sLORETA are z-scores (when source orientation is fixed apriori).


Regards,
Hari



On Wed, June 1, 2011 5:58 pm, Mingbo Cai wrote:
> Hi Alexandre and Eric,
> Thanks very much.
>
> Attached are my scripts. Usually what I do is first use mne_browse_raw to
> look at each epoch and remove the epochs that seem to have eye blinking in
> the event list. Then run meg_process1_2.tcsh which calls ave_cov_2.tcsh
> and meg_setup.tcsh. After that I align MRI and sensors in mne_analyze and
> then run meg_process2_2.tcsh. When I reanalyze the data, I commented out
> the meg_setup part and did not align. Just run meg_process1_2.tcsh and
> meg_process2_2.tcsh separately.
>
> Each subject has a folder, in which MEG data are saved in a folder called
> meg, other folders are generated by freesurfer. When I run my script, I
> call a for loop to pass the subject id to the script as the first
> parameter. The environment variable SUBJECT is only set within the script,
> but not before I call the script. Could this cause problem?
>
> Another question is, it seems to me that sLORETA is influenced by the
> number of trials while MNE is not (the sLORETA response of all trials is
> larger than that of every subset of the trials) . When you average across
> subjects, which one do you prefer to average?
>
> Thanks
>
>
> Mingbo Cai
>
>
>
> -----Original Message-----
> From: Alexandre Gramfort [mailto:gramfort at nmr.mgh.harvard.edu]
> Sent: Wed 6/1/2011 2:57 PM
> To: Mingbo Cai
> Cc: mne_analysis at nmr.mgh.harvard.edu
> Subject: Re: [Mne_analysis] Do I need to setup mri and do watershed etc
> procedure every time I re-analyze the data
>
> Hi,
>
>> As my understanding from the Fig 3.1 of the manual (the workflow), the
>> steps
>> of mne_setup_mri, alignment, mne_watershed, mne_setup_forward_model are
>> independent from the calculation of average and noise-covariance.
>
> correct.
>
>> On the
>> other hand, it seems that only in the averaging and noise covariance
>> steps I
>> need to explicitly use the SSP, I thought I could do only the averaging
>> and
>> noise covariance calculation without the above steps, and use the bem
>> and
>> surface files generated in the last analysis to go on to
>> mne_do_forward_solution and mne_do_inverse_operator. However, after I
>> did
>> these, in the mne_analyze interface, it did not allow me to view the
>> source
>> estimate on the surface (whenever I click on the timecourse manager
>> window,
>> it pops up to say "Surfaces do not match the source spaces. Cannot
>> display
>> estimates.") But when i click on the surface, the signal of that vertex
>> can
>> be displayed in the bottom-left window.
>
> it means vertices in your source space are not present in the surface.
> Are you sure you properly defined the SUBJECT and that you did not mess
> with this part?
>
>> When I checked the log file of the outputs of the
>> mne_do_forward_solution
>> and mne_do_inverse_operator from the two times of analysis, it seems
>> there
>> are no difference except for the part of SSP and the SVD result due to
>> that.
>> All the correct files are used when I redo the analysis.
>
> SSP is independent of the source space and the forward operator.
> So it is a bit weird.
>
>> Does any one has a clue of what is the reason? And am I right that I do
>> not
>> need to redo those early steps if I only want to add SSP in my analysis?
>
> that's right.
>
> maybe you can share the lines you used in your analysis. We might be able
> to spot a pb in your pipeline.
>
> Alex
> --
> Alexandre Gramfort, PhD
> gramfort at nmr.mgh.harvard.edu
> Dept. of Radiology MGH Martinos Center / Harvard Medical School
> http://www-sop.inria.fr/members/Alexandre.Gramfort/
>
>> Thanks very much
>>
>>
>> Mingbo Cai
>> Department of Neuroscience
>> Baylor College of Medicine
>>
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-- 
Hari Bharadwaj