[Mne_analysis] Cortical labels power spectrum different approaches

[Peled, Noam]

Hey Alex,

Yes, you can find the script here<https://github.com/pelednoam/mmvt/blob/master/src/misc/power_spectral_density.py>.

It's based on this mne example<https://martinos.org/mne/stable/auto_examples/time_frequency/plot_compute_source_psd_epochs.html>.

One thing the pops immediately, is that only on the second approach (psd_array_multitaper on the label_ts) you need to set the mode (I set it to mean_flip)

Also, for both of them, I use 10 * np.log10(x) to get dB. Not sure this correct in the first approach, mostly because it's not part of the mne example.


Thanks,

Noam

________________________________
From: mne_analysis-bounces at nmr.mgh.harvard.edu <mne_analysis-bounces at nmr.mgh.harvard.edu> on behalf of Alexandre Gramfort <alexandre.gramfort at inria.fr>
Sent: Thursday, August 30, 2018 9:27:59 AM
To: Discussion and support forum for the users of MNE Software
Subject: Re: [Mne_analysis] Cortical labels power spectrum different approaches

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hi,

It should be more in agreement.
Can you share a script on one of the MNE datasets to figure out the
cause of the difference?
Also note that both units in your plots are very different (dB vs I am not sure)

Alex

On Wed, Aug 29, 2018 at 11:18 PM Peled, Noam <NPELED at mgh.harvard.edu> wrote:
>
> Let me be more specific/clear:
>
> I'm analyzing data from a patient with an ECOG. I want to compare the power-spectrum of the electrodes and the MEG cortical labels I've created around each electrode.
>
> It seems that calculating the time series in the source space of long enough MEG epochs (~10s), split the electrodes file to same length epochs, and use
>
> mne.time_frequency.psd_array_multitaper on both of them is the way to go, and also I know that both are in the same units (10*log10 for [dB]).
> But I'm still a little bit confused by the different results I'm getting when using mne.minimum_norm.compute_source_psd_epochs instead.
>
> Thanks,
> Noam
>
> ________________________________
> From: mne_analysis-bounces at nmr.mgh.harvard.edu <mne_analysis-bounces at nmr.mgh.harvard.edu> on behalf of Peled, Noam <NPELED at mgh.harvard.edu>
> Sent: Wednesday, August 29, 2018 2:32:39 PM
> To: mne_analysis at nmr.mgh.harvard.edu
> Subject: [Mne_analysis] Cortical labels power spectrum different approaches
>
>
> Hey all,
>
> I'm calculating MEG cortical labels power spectrum (for resting state data) in two different ways. Can you help me understand the differences? The power spectrums are quite different (see attached).
>
>
> 1) Go through the source space time-series:
>
>
> stcs = mne.minimum_norm.apply_inverse_epochs(epochs, ...)
> labels_ts = mne.extract_label_time_course(stcs, labels, ...)
> for label_ts:
>   psds, freqs = mne.time_frequency.psd_array_welch(label_ts, ...)
>   psds = 10 * np.log10(psds)
>
>
> 2) Compute the PSD from the epochs:
>
>
> for label_ind, label in enumerate(labels):
>   stcs = mne.minimum_norm.compute_source_psd_epochs(epochs, ...)
>   for stc in stcs:
>     psds = np.mean(stc.data, axis=0)
>
>
>
> Thanks!
>
> Noam
>
>
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