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

[Mingbo Cai]

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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