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

[Hari Bharadwaj]

I would add that the issue of having the software machinery to potentially try localizing deep sources is a separate issue from trusting the obtained solution..Thus, for the purposes of demos and code development, localizing simulated deep source activity might be the best scenario where the ground truth is known..

If real data demos are really desired, something like the ABR might be a potentially  safer candidate...



"Ghuman, Avniel" <ghumana at upmc.edu> wrote:

>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
>>>>>> 
>>>>>> 
>>>>>> _______________________________________________
>>>>>> 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.
>>> _______________________________________________
>>> 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
>> 
>> 
>> _______________________________________________
>> 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

-- 
Sent from my Android phone with K-9 Mail. Please excuse my brevity.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20140526/6ffdb809/attachment.html