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

Gladia Hotan gladiach at gmail.com
Fri Jul 1 10:10:27 EDT 2016
Search archives:

Hi Denis,

I tried replacing stc.data and stc.times as such:

stc._data = stc.data[0]  # Just look at the first frequency
stc.times = stc.times[0]

But trying to plot this gives 'ValueError: dimension mismatch'. Could you
explain a bit more about how I should hack the stc object? Also, how do I
figure out how much to scale the data by?

Thank you and Best Regards,
Gladia

On Thu, Jun 30, 2016 at 4:55 PM, Denis-Alexander Engemann <
denis.engemann at gmail.com> wrote:

> I can answer in greater detail later, but 1) you need to "hack" the stc
> object and figure out the right scale after putting the frequenies in
> .times and accordingly scale ; by default our data containers assume time
> domain data 2) if you use dSPM as method it is a pseudo F-statistic, for
> interpretable power plots you should use MNE as method in the inverse
> solver
>
> I hope this helps a bit,
>
> Denis
> On Thu, 30 Jun 2016 at 22:49, Gladia Hotan <gladiach at gmail.com> wrote:
>
>> Hi,
>>
>> I have a couple of questions about the psd of sources:
>>
>> 1) I used
>>
>> stc = mne.minimum_norm.compute_source_psd
>>
>> to get an stc file containing the psd of the sources. It seems like in this stc file,
>> frequency has replaced time, but is still called 'time':
>>
>> <SourceEstimate  |  ... tmin : 0.0 (ms), tmax : 55.0 (ms), tstep : 0.25 (ms) ...>
>>
>> (I set the function to compute from 0 to 55 Hz; the time duration of the data is
>> actually a lot longer). I can use stc.plot or mne.plot_source_estimates to visualize this, but it treats
>> the frequencies like times. How can I plot the psd at a particular frequency on the brain?
>>
>> 2) What are the units of the psd of the sources? According to the tutorial <http://martinos.org/mne/stable/auto_examples/time_frequency/plot_source_power_spectrum.html#sphx-glr-auto-examples-time-frequency-plot-source-power-spectrum-py> the psd is in dB,
>> but what is the reference quantity being used when converting to dB? (Ie. what is Pref in P_db = 10*log10(P/Pref)?)
>> Am I right that the source amplitudes are in units of ampere-metres?
>>
>> Thanks and Best,
>> Gladia
>>
>> _______________________________________________
>> 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
>
>
> 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.
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20160701/2dc637a2/attachment.html 


More information about the Mne_analysis mailing list