[Mne_analysis] Visualizing power spectrum density of sources on the brain

[Denis-Alexander Engemann]

Sorry Gladia,

I was a bit unclear I fear. I was referring to the fact, that if you want
to see things in dB and want to look at the power spectrum in one ROI or
vertex the same way you want to look at it in the sensor space, you need to
use the MNE option. You can then intuitively take the decadic logarithm and
scale to dB.
Then for the surface plotting it is a bit tricky with regard to color maps.
Both dSPM and MNE can be intuitively used but the entire MNE viz system
sort of expects time domain data as you may have noticed, where data are
dont' have any tend.
With frequency domain data this is not the case, you have local peaks but a
global 1/f trend which will mess up your display. You then either need to
detrend the spectrum or choose fmin, fmid, fmax, carefully, essentially
setting them at each frequency where you make sure that your stc.times
vector is not longer than 1; by default histograms for determining viz
values are computed over all time points so the auto option won't work.
Lot's of manual tuning required unfortunately.
As to your plots I'm not fully sure I get your message. Intuitively make
sure you get the relationship between the time domain and the specteal data
right, maybe the time domain localization is driven by a certain band. And
as said, colormaps can be difficult and misleading. Plotting historgrams
along the way and looking at slices can help understand what you do.

I hope this helps a bit,
Denis


On Thu, Jul 7, 2016 at 4:04 PM Gladia Hotan <gladiach at gmail.com> wrote:

> Thanks Alex!
>
> I am wondering why when I plot the psd on the brain I get a lot of
> activity in the corpus callosum and white matter rather than in the grey
> matter, which is where the sources are localized to. Here is a link to
> example screenshots of the source distribution vs the psd distribution on
> the brain, which don't seem to match:
> https://www.dropbox.com/sh/blstn3xitewbg5t/AACia--q9mF6d0ZjluhXq_TGa?dl=0
>
>  How can I check that the source psd is being plotted correctly?
>
> Thanks and Best,
> Gladia
>
>
> On Tue, Jul 5, 2016 at 4:54 PM, Alexandre Gramfort <
> alexandre.gramfort at telecom-paristech.fr> wrote:
>
>> > Could anyone explain why MNE should be used instead of dSPM to get the
>> power
>> > plots? The tutorial on the MNE website says to use dSPM as the solver.
>>
>> dSPM is just a normalized/scaled version of MNE (scaling is obtained
>> form the noise standard deviation derived from the noise cov). So
>> basically it's just a scaling factor. If you apply a baseline /
>> contrast with a log ratio of power then there is no diff between the
>> 2.
>>
>> HTH
>> Alex
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