requesting support - Power Spectra Interactive model

[Pragha]

Dear TVB user,

I tried to calculate the power spectrum for the simulated data. Please find the attachment of my code.  I guess that I have defined all the required parameters but I do get errors while executing. Could some help where I went wrong?

Thank you,

Pragha

[Julie Courtiol]

Dear Pragha,

The error informs you there is a shape problem with your data. Indeed, the TimeSerieRegion requires data in TVB format, i.e., 4D:

TAVG = TAVG[:, numpy.newaxis,:,numpy.newaxis]

Then, you can define

tsr.data = TAVG

Best,

Julie

Dr. Julie Courtiol

Scientific Lab Manager

Brain Simulation Section 

Charité Universitätsmedizin Berlin

Le 17 août 2021 à 15:33, Pragha <praa...@gmail.com> a écrit :



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<PowerSpectrum.pdf>

[Pragha]

Thank you. But it is showing the same error after converting the data into 4d. Do I need to check something ?

[Julie Courtiol]

Hi Pragha,

Try with this:

psi = ps_int.PowerSpectraInteractive()
psi.time_series=tsr

psi.period=0.001 #s

Be careful, the tsr sampling period is in ms.

Also, I advise you to separate your code in several cells to debug it and see where the error is.

---

Best regards,

Julie Courtiol

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[Julie Courtiol]

Dear Pragha,

I had a deeper look into the code and found why the function (psi.configure) returns an error. I will give you the correction below (and the file to replace in your tvb folder).

See also some comments on your code.

[4]: You don't need to define S, C and dS.

They were only defined for building the phase plane in the tutorial. Here, as you can see you are not using these variables.

[5] Úseless as you are already running the simulation in the previous cell (>> (time, data), = sim.run())

[14] The sampling period is wrong. It is also in ms!

#Create a tvb TimeSeries object
tsr = TimeSeriesRegion(connectivity=con,
                       data=tavg,
                       sample_period=sim.monitors[0].period)
tsr.configure()

Also, to identify the error easily, I advise you to separate your code lines in separated cells.

For psi, you need to define it as the TimeSeries above:

#Create and launch the interactive visualiser
psi = ps_int.PowerSpectraInteractive()
psi.time_series=tsr

For the psi.configure(), I have implemented some corrections in the code

line 159: convert the sampling period in second for further use 

lines 328 and 352: seg_tpts, starts and nfreq are float and need to be converted in integer

When you then run your notebook, you should obtain a similar figure

Best,

Julie

---

Best regards,

Julie Courtiol

[Pragha]

Dear Dr. Julie Courtiol,

Many thanks for the support. 

Best,

Pragha

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