[Mne_analysis] Query over medial wall activity

Sat Feb 9 16:10:20 EST 2013

hi everyone,

just a quick note. The SNR used in dSPM extends the spread. If you have
high SNR data you should reduce these "ghost sources". It would worth
performing a simulation to see what's a good SNR to avoid this. Also
now that mne-python has LCMV beamformer it'd be curious to see
how much this will happen too (it should at a certain level).

Cheers,
Alex

On Thu, Feb 7, 2013 at 8:23 PM,  <acgt2 at cam.ac.uk> wrote:
> Hi everyone,
>
> I have done the reconstruction for a simulation of Heshls Gyrus activity and
> I end up with Figure 1 (attached), which confirms the findings of Pavan,
> namely that sources simulated in Heshls Gyrus can end up (very strongly) on
> characteristic parts of the medial wall [1]. I can confirm that the
> positioning of this activity is identical to where I find my medial wall
> matches. From the comments so far, this seems to be a wide spread
> phenomenon.
>
> As Don suggests, this doesn't necessarily mean that all medial wall activity
> found is erroneous, but I feel it more than likely that, in my particular
> case, it seems misleading to portray my medial wall matches as correct,
> given that I have strong prior reasons from the literature to believe that
> HG activity is correct.
>
> As I see it, there are a couple of options open to those that find strong
> spread from HG (or other areas) onto the medial wall. Please tell me if you
> don't agree with these, or if you think there are other options :-)
>
> 1.      Exclude 'unknown' and other medial regions from the final analysis,
> saying that the reconstruction mislocalises 'real' activity to this area.
> But this is a bit difficult - who is to say which area is prone to
> mislocalisation and which isn't? The medial wall isn't the only place that
> simulated activity mislocalises too - one could use the same logic to cut
> out any regions one didn't want to see activity in. As I mention above, I
> might be OK claiming this, but only because I have strong evidence from the
> literature that tells me HG is correct (and thus that HG is mislocalising to
> 'unknown', and not the other way around).
>
> 2.      Do what Dan suggests and exclude this area from the forward
> solution. This would have the added advantage that it would presumably make
> the resulting reconstruction more accurate. But one would need to be pretty
> sure that the sensors aren't (ever) picking up medial wall activity (or at
> least, only very weakly), because once it's gone, true medial activity is
> then localised to the lateral surface. As Dan points out, perhaps we might
> justify this by assuming there aren't sufficient pyramidal dendrites in this
> region, but Don has cautioned that sensors might pick up medial transient
> longitudinal currents. I would be very interested to hear any further views
> on this.
>
> 3.      Further priors of some sort, perhaps related to physiology of the
> medial wall. But this would require some sort of agreement of number 2.
>
> Hope his is helpful, thanks for all your thoughts so far,
>
> Andy
>
> [1] the 'no depth' option was present in this reconstruction.
>
> -----Original Message-----
> From: mne_analysis-bounces at nmr.mgh.harvard.edu
> [mailto:mne_analysis-bounces at nmr.mgh.harvard.edu] On Behalf Of
> acgt2 at cam.ac.uk
> Sent: 07 February 2013 11:23
> To: mne_analysis at nmr.mgh.harvard.edu
> Subject: Re: [Mne_analysis] Query over medial wall activity
>
> Hi everyone,
>
> Many thanks for all your thoughts so far. Sheraz - will test this and post
> my results to this list, hopefully later today.  As I understand it from his
> email, Pavan's ghosting appeared when simulating a source in auditory cortex
> - so, as a first step, let's see if I can replicate that. I'll try and look
> at a small cross-section of lateral vertices.
>
> Perhaps also worth mentioning, as I didn't put it in the original email - I
> also did some MEG-only and EEG-only reconstructions to see which information
> is contributing greatest to this (real or unreal) 'ghosting effect', and it
> seems to be EEG. This doesn't seem to me to invalidate one view or another -
> as I understand it, EEG is better at picking up deep sources, with some
> groups using EEG to record brainstem responses (although this effect
> requires thousands of trials to become reliable); on the other hand, 'EEG is
> better at localising deep sources' is another way of saying 'MEG is worse at
> localising deep sources',  so if this effect is a mislocalisation to the
> medial wall then perhaps it is not surprising that MEG is not contributing
> as much to it.
>
> Anyway, will report back later with results.
>
> Andy
>
>
> -----Original Message-----
> From: sheraz at nmr.mgh.harvard.edu [mailto:sheraz at nmr.mgh.harvard.edu]
> Sent: 06 February 2013 23:20
> To: A.C.G. Thwaites
> Cc: mne_analysis at nmr.mgh.harvard.edu
> Subject: Re: [Mne_analysis] Query over medial wall activity
>
> Hi Andy,
>
> Best solution to find out, your activity on medial wall is real or not, put
> a simulated source on Heshl's Gyrus of apropriate size, multiply it with the
> forward operator and then add some empty room noise to it. Solve again the
> inverse solution to find the spread.
>
> This can be done easily in mne-matlab or mne-python.
>
> Sheraz
>
>
>
>
>> Hi MNE-ers
>>
>>
>> I am working with auditory data, running my analysis on source
>> estimations reconstructed from MEG and EEG sensor recordings.
>>
>>
>> My analysis takes the form of pattern matching over the estimated
>> activity of each of the vertices in a source space, and as such, is
>> reliant on the reconstruction being of good quality. I am very pleased
>> with the quality of the results using MNE - my pattern matching
>> technique should locate those vertices along Heshl's Gyrus, and indeed
>> it does - an indication, presumably, of the high quality of the
>> reconstruction. (so a big thank you to everybody involved with
>> constructing and maintaining MNE!)
>>
>>
>> However, I did want to ask this mailing list about one concern: my
>> pattern matching technique also picks up vertices directly 'under' HG
>> - on the medial wall in the 'unknown' label of the Destrieux Atlas
>> (aparc.a2009s.annot) (see figure 1 attached). It seems pretty clear why:
>> the inverse solutions given by MNE give both these regions similar
>> evoked responses (figure 2 of the attached), which is why my pattern
>> matching technique flags both areas up. While it is possible that
>> these results may be correct (the auditory thalamus is in this area,
>> and so might plausibly causing this medial activity) I wanted to poll
>> this mailing list to get a feel for how likely you think this activity
>> is being correctly estimated here, or if you feel it is a simple case
>> of mislocalisation from the auditory cortex (and if so, whether it can
>> be fixed). I'm not really sure what my grounds for suspicion are,
>> except that the affected vertices on the medial wall are directly
>> under HG - implying the HG source activity might be 'seeping' through
>> to these more medial sources during reconstruction.
>>
>>
>> I have observed this phenomenon in two independent experiments. And
>> although I can't do my pattern matching on the MNE example 'audvis'
>> data, this too seems to show the same phenomenon (figure 3).
>>
>>
>> I have tried pretty much every flag and option MNE offers - depth
>> on/off, sLORETA vs. MNE vs. DSPM, different SNRs, pick_normal on/off,
>> different looseness's - all end up with pretty much identical results
>> (which is good, I guess, as it means the reconstruction is pretty robust).
>>
>>
>> I appreciate that for many people this isn't an issue if they are
>> doing analysis only in predetermined regions of interest (I can't
>> imagine that many people are looking for results in a label called
>> 'unknown'). But as my analysis works by searching vertex-by-vertex, I
>> want to say truthfully that I looked through all vertices the
>> reconstruction gave back, or at least give a reason why I excluded
>> vertices in the `unknown' label from my analysis.
>>
>>
>> Anyway, I don't know if it is a common occurrence, or is something I
>> have done wrong (although the fact that we see the 'audvis' data
>> behave in the same way is evidence against this). Or maybe you think
>> it is correct - a number of my co-authors have suggested we take it as
>> correct, and say it is evidence of a cortico-Thalamic loop.
>>
>>
>> I attach some figures that demonstrate the phenomenon.
>>
>>
>> Thanks in advance for any thoughts.
>>
>>
>> Andy
>>
>>
>> _______________________________________________
>> Mne_analysis mailing list
>> Mne_analysis at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail contains patient information, please contact the Partners Compliance
> HelpLine at http://www.partners.org/complianceline . If the e-mail was sent
> to you in error but does not contain patient information, please contact the
> sender and properly dispose of the e-mail.
>
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in error
> but does not contain patient information, please contact the sender and properly
> dispose of the e-mail.
>