[Mne_analysis] Alarmingly similar results for subcortical source activity

[Ghuman, Avniel]

Hi Alan,

I am not sure why you would expect to get something different for the two
cases. We have compared volume based analyses with cortex only analyses
and they are nearly identical (as they should be assuming little of the
sensor signal is coming from non-cortical sources). Thus, I would agree
with Alex, the key now is simulations. The critical questions are:

1. if there is a source in the amygdala, but not on the cortex, can you
see it and how much cortical bleed is there?

2. If there is a source nearby in the cortex, but not in the amygdala, how
much bleed into the amygdala is there?

Hope that is helpful.

Best wishes,
Avniel


On 6/3/14 5:52 PM, "Alexandre Gramfort"
<alexandre.gramfort at telecom-paristech.fr> wrote:

>Hi Alan,
>
>I don't see any obvious mistake in your scripts and the results
>don't surprise me much due to field spread.
>
>The line that bothers me is:
>
>forward = mne.convert_forward_solution(forward, surf_ori=True)
>
>There should not be any source orientation constraint for
>deep structures.
>
>Simulation is indeed the way to go now I would say.
>
>Alex
>
>
>On Tue, Jun 3, 2014 at 2:13 AM, Alan <leggitta3 at gmail.com> wrote:
>> Hello,
>>
>> I've been looking at right amygdala activity in the spm faces dataset
>>as a
>> means of developing subcortical source localization tools. I've tried
>>two
>> different methods so far.
>>
>> 1.) I did a whole brain volume analysis (dSPM) and then averaged
>>together
>> vertices belonging to the right amygdala (code here).
>>
>> 2.) I merged the left and right cortical surface source spaces with a
>>right
>> amygdala volume source space, performed dSPM and then averaged together
>>the
>> volume sources (code here).
>>
>> I've attached the evoked plots for each condition (grey bars indicate
>> regions of significant difference using independent t-tests per time
>>point
>> with fdr correction).
>>
>> The results of each method are so similar that I'm concerned they may be
>> derived from a common source of error. Can anyone think of think of any
>> probable sources of error and suggest other ways to validate these
>>methods?
>> I haven't yet ventured into simulated data, but I think that's going to
>>be
>> the next step.
>>
>> Thanks!
>> Alan
>>
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