[Mne_analysis] Query over medial wall activity

Tue Feb 12 11:00:15 EST 2013

Hi all,

One factor I believe has not not been mentioned is that the correction of depth bias induced by converting MNE into dSPM is somewhat too aggressive and, therefore, 
you are likely to get these false activations in the medial wall. Note also that the medial surface of the temporal lobe is not so terribly far from the auditory areas in the Sylvian fissure. 

Best,
- Matti

On Feb 12, 2013, at 10:31 AM, <acgt2 at cam.ac.uk> <acgt2 at cam.ac.uk> wrote:

> Hi Alex,
> 
> Thanks for this. Regarding SNR - I am working with single trials and I get
> the best results when I specify an SNR of 1, so this could be exacerbating
> the ghosting problem for me. However, the example plots I gave as mock ups
> were of grand averages, where I specified an SNR  of 3. I might do a test
> where I make it higher value to see if this improves things.
> 
> With regards to the LCMV beamformer, I will perform this shortly, both on my
> data and the example mne audvis_data, and post it to the list.
> 
> I will also try excluding the 'unknown' region from my forward model to see
> what this result looks like (independent of whether any of us think it is a
> good idea), and post the result to the list.
> 
> Cheers,
> 
> Andy
> 
> -----Original Message-----
> From: Alexandre Gramfort [mailto:gramfort at nmr.mgh.harvard.edu] 
> Sent: 09 February 2013 21:10
> To: acgt2 at cam.ac.uk
> Cc: mne_analysis at nmr.mgh.harvard.edu
> Subject: Re: [Mne_analysis] Query over medial wall activity
> 
> 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
>> 
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---------

Matti Hamalainen, Ph.D.
Athinoula A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital

msh at nmr.mgh.harvard.edu
mhamalainen at partners.org

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