[Mne_analysis] extracting ROI sources using mne_compute_raw_inverse

Hari Bharadwaj hari at nmr.mgh.harvard.edu
Wed Oct 19 12:48:19 EDT 2011
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Hi Matt,
   I'm not sure if the implementation of mne_compute_raw_inverse ignores
the --align_z flag if (1) --picknormalcomp is used and/or if (2) Your
source space contains sources of fixed orientation... So unfortunately,
I don't have a better suggestion than to try leaving out the
picknormalcomp option or if you are using a fixed orientation solution
try loose..

I can share python code (that's not tested much) that works with a fixed
orientation inverse operator if you are interested in playing with it..

Regards,
Hari



On Wed, October 19, 2011 12:09 pm, Matt Panichello wrote:
> Hi Hari,
>
> Thanks for your response. I had included the --align_z flag with
> mne_compute_raw inverse, so unfortunately I don't think this is the issue.
> Do any other possibilities come to mind?
>
> This is a shot in the dark on my part, but the script I inherited for this
> analysis also included the --picknormalcomp flag with
> mne_compute_raw_inverse. Could this be causing trouble for any reason?
>
> Thanks again,
>
> Matt
>
>
> On Tue, Oct 18, 2011 at 6:24 PM, Hari Bharadwaj
> <hari at nmr.mgh.harvard.edu>wrote:
>
>> Hi Matt,
>>   This is just a hunch.. So in viewing using mne_analyze, for the
>> options
>> you have selected you are averaging the absolute value of the signal
>> across vertices.. On the other hand when using mne_compute_raw_inverse,
>> you seem to be doing a signed averaging (Which is the correct thing to
>> do given you want to do frequency analysis). What happens when you
>> average the signed signal across vertices is that since the orientation
>> of the sources is not the same and the MNE spreads, some vertices have
>> positive polarity deflections and some have negative polarity
>> deflection and they cancel.. The avoid this cancellation there is a
>> --align_z option  in mne_compute_raw_inverse that you could use which
>> is described in the manual.
>>
>> Hope it helps,
>>
>>
>> Regards,
>> Hari
>>
>>
>> On Tue, October 18, 2011 6:02 pm, Matt Panichello wrote:
>> > Hi everyone,
>> >
>> > I am trying extract the sources from a series of functional-anatomical
>> > rois
>> > for frequency analysis, but am having some trouble getting good
>> quality
>> > data. I'm using mne_compute_raw_inverse to extract the data before
>> loading
>> > it into matlab.
>> >
>> > Subjects completed an object recognition task during recording. To
>> check
>> > the
>> > quality of the extracted data, I've been averaging the timecourses in
>> an
>> > early visual ROI across all vertices and visualizing the evoked
>> response.
>> > For some of the subjects (e.g., S003-a, attached), the evoked response
>> > looks
>> > normal. The evoked response for many subjects, however, looks like
>> > senseless
>> > noise (S007-a) or shows an unexpected negative deflection (S010-a).
>> >
>> > I don't think these problems are solely due to the labels I've drawn,
>> or
>> > to
>> > the intrinsic quality of the raw data. This is because when I average
>> the
>> > raw data for each subject using mne_process_raw, and then view the
>> average
>> > of the vertices inside the same ROIs using mne_analyze, the evoked
>> > responses
>> > all look as expected, often very different from the averages produced
>> from
>> > my mne_compute_raw_inverse pipeline (see S007-b and S010-b).
>> >
>> > Does anyone have an idea what the problem might be? Are there any
>> special
>> > considerations to take in account when using mne_compute_raw_inverse
>> to
>> > extract sources from ROIs? Why might the label averages using the two
>> > different methods described look so different?
>> >
>> > Thanks in advance for any help,
>> >
>> > Matt
>> > _______________________________________________
>> > Mne_analysis mailing list
>> > Mne_analysis at nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>
>>
>> --
>> Hari Bharadwaj
>>
>>
>>
>>
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>
>
> --
> Matthew Panichello
> Research Coordinator, Bar Group
> Massachusetts General Hospital
> Phone: 617-726-9034
>


-- 
Hari Bharadwaj



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