[Mne_analysis] calculating phase locking values on MNE source estimate within labels- using mne.minimum_norm.source_induced_power

[Alexandre Gramfort]

hi David,

see inline comments

>  I am trying to render a a time- frequency map containing phase locking
> values (0-1) from label files containing SVD’s of  MNE source estimate
> timeseries. I began with the example:
>
> https://martinos.org/mne/stable/auto_examples/time_frequency/plot_source_label_time_frequency.html#sphx-glr-auto-examples-time-frequency-plot-source-label-time-frequency-py
>
> which gives ITC for evoked plus induced and induced alone using
> mne.minimum_norm.source_induced_power. my questions are the following
> parameters:
> If I choose  baseline =None  and baseline_mode=None, will I get PLV values
> of 0-1 across all the epoch where the locking is relative to stimulus onset
> (i.e. at time zero).

yes

> 2) zero_mean   when should this be used? are all wavelets not zero-meaned by
> default?

very often Morlet wavelets are used in Neuroscience without the \kappa_\sigma
in defintion from https://en.wikipedia.org/wiki/Morlet_wavelet

this constant makes sure the wavelets are zero mean.

it's not a big problem if you use many cycles (lets say > 5) but otherwise
your wavelet coefficient will capture a DC component.

Historically I had written the code without the \kappa_\sigma and when I added
it, I made it an option with zero_mean. I suggest to always use zero_mean=True.

> 3)  the parameter prepare: When calling a saved inverse operator file at the
> beginning of a script like the example as in my caee executing the full
> inverse_operator = read_inverse_operator(inv_fname)
> src = inverse_operator['src’]  initially  and then looping thought the
> labels. Can setting the Prepare’= True be done and will it save time?

yes if you prepare the inverse operator you should save time.

HTH
Alex


> thanks in advance
>
>
> david
>
>
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