[Mne_analysis] GSoC Update: dSPM source reconstruction for the right amygdala in the SPM dataset

[Ghuman, Avniel]

I should say though, things like Hippocampus and cerebellum might be more feasible.

> On May 26, 2014, at 5:33 PM, "Ghuman, Avniel" <ghumana at upmc.edu> wrote:
> 
> It also might be a reasonable time to discuss a bit of the physics and physiology of what MEG is and is not sensitive to. MEG is not particularly sensitive to four things:
> 
> 1. Radial sources
> 2. Deep sources
> 3. Sources where the neurons are not aligned
> 4. Even worse are sources with randomly aligned neurons that are relatively spherical (and small)
> 
> The amygdala strikes out on the bottom three. Thus, in my opinion, it is fairly unlikely that MEG can pick up activity from the amygdala. I would love to hear other opinions.
> 
> Best wishes,
> Avniel
> 
> Avniel Ghuman, Ph.D.
> Director of MEG Research
> Assistant Professor of Neurological Surgery, Neurobiology, and Psychiatry
> Faculty in the Center for the Neural Basis of Cognition
> University of Pittsburgh
> 
> ________________________________________
> From: mne_analysis-bounces at nmr.mgh.harvard.edu [mne_analysis-bounces at nmr.mgh.harvard.edu] on behalf of sheraz at nmr.mgh.harvard.edu [sheraz at nmr.mgh.harvard.edu]
> Sent: Monday, May 26, 2014 5:13 PM
> To: Discussion and support forum for the users of MNE Software
> Subject: Re: [Mne_analysis] GSoC Update: dSPM source reconstruction for the right amygdala in the SPM dataset
> 
> hi Alex,
> 
> my 2 cents, if you look at the waveform carefully, the responses follows
> the same time course as the cortical responses. Putting this example will
> give very wrong impression about MEG and deep sources.
> 
> Putting premature examples might not be great idea :)
> 
> Sheraz
> 
>> hi Alan,
>> 
>> if the demo aims to demonstrate inverse modeling with deep structures
>> I would put it in examples/inverse
>> 
>> Alex
>> 
>> 
>>> On Mon, May 26, 2014 at 9:00 PM, Alan <leggitta3 at gmail.com> wrote:
>>> Hi Alex,
>>> 
>>> Thanks. I will make that my next step. Where in the mne code structure
>>> should I put this? I was thinking in under examples/datasets.
>>> 
>>> Alan
>>> 
>>> 
>>> On Sat, May 24, 2014 at 5:43 AM, Alexandre Gramfort
>>> <alexandre.gramfort at telecom-paristech.fr> wrote:
>>>> 
>>>> hi Alan,
>>>> 
>>>> nice work !
>>>> 
>>>> I have a few comments to make on the code so a PR on github would allow
>>>> me to comment inline.
>>>> 
>>>> Regarding the approach, it does what it is supposed to do in a pretty
>>>> elegant way, but
>>>> it is dangerous to only run the inverse method on such a tiny
>>>> source space. An activation from the cortex would necessarily be
>>>> projected
>>>> to the amygdala. My hunch, is that an LCMV beamformer would suffer
>>>> less from this.
>>>> 
>>>> I think the next step would be to be able to combine a surface source
>>>> space
>>>> and the deep volume source space you create.
>>>> 
>>>> best,
>>>> Alex
>>>> 
>>>> 
>>>>> On Sat, May 24, 2014 at 1:10 AM, Alan <leggitta3 at gmail.com> wrote:
>>>>> Hello,
>>>>> 
>>>>> I worked through creating a discrete source space of the right
>>>> amygdala
>>>>> and
>>>>> performing dSPM source reconstruction in the SPM dataset. My code is
>>>>> available on my GSoC blog.
>>>>> 
>>>>> 
>>>>> http://misterbrainley.blogspot.com/2014/05/day-5-putting-it-together.html
>>>>> 
>>>>> I've attached a copy of the results for data filtered between 1-45
>>>> hz.
>>>>> The
>>>>> grey region indicates statistical significance using an independent
>>>>> t-test
>>>>> with fdr correction.
>>>>> 
>>>>> I would greatly appreciate any feedback you could offer.
>>>>> 
>>>>> Thanks!
>>>>> Alan
>>>>> 
>>>>> 
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