[Mne_analysis] Alarmingly similar results for subcortical source activity

[Alan]

Thanks Alex and Avniel,

I'll get started on trying to generate simulated data.


Alex,

I think I was getting an error when I didn't include the line

>forward = mne.convert_forward_solution(forward, surf_ori=True)

But I can dig deeper into that.

-Alan


On Tue, Jun 3, 2014 at 3:09 PM, Ghuman, Avniel <ghumana at upmc.edu> wrote:

> 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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