[FieldTrip] About source reconstruction outputs

[Fabio Strappazzon]

Many thanks!

On Wed, 17 Dec 2025, 15:40 ivano triggiani, <ivanotriggiani at gmail.com>
wrote:

> Let's see...
> If you use pwelch per x,y, and z, you are basically calculating the power
> spectrum (which is related to the squared magnitude of the Fourier
> transform), so I doubt it's correct to square them again.
> I know somebody uses the average, which is a possibility, but it can
> underestimate the total spectrum.
> The correct solution (again, it can look weird) should technically be the
> sum of the 3 PSDs, which are already squared, so Ptot(f)=Px(f)+Py(f)+Pz(f)
> is the vector sum and should be the correct solution.
>
> Everyone feels free to correct me if I am wrong.
>
> Ciao,
>
> Ivano
> ---
>
> *A. Ivano Triggiani, Ph.D.*
>
>
> ________________________________________________
>
>
>
> On Wed, Dec 17, 2025 at 6:50 AM Fabio Strappazzon <fab.strappaz at gmail.com>
> wrote:
>
>> Ciao Ivano,
>> thank you for your anwer.
>>
>> 1) As expected, thanks.
>>
>> 2) Your solution would be fine but the problem is that for each dipole I
>> have a 3 x pnts array (orientation x time points) and I do not know how
>> FieldTrip would take care of that. But even trying to using classical
>> MATLAB function like pwelch (as I'm curretly doing) I'm not super sure how
>> should I proceed: should I calculate a separate PSD for orientation? And
>> then what: summing across orientation? Taking the average? Taking the
>> squared root of sum?
>>
>> Thank you for your help
>>
>> Il giorno mar 16 dic 2025 alle ore 22:44 ivano triggiani <
>> ivanotriggiani at gmail.com> ha scritto:
>>
>>> Caro Fabio,
>>>
>>> My humble opinion:
>>>
>>> 1. Since source reconstruction is a well-known ill-posed problem, every
>>> method relies on different constraints. For instance, MNE minimizes the
>>> overall L2 norm, which often results in smooth solutions, easily distorted
>>> if noise is significant.
>>>
>>> To stabilize the solution, regularization methods use, for example,
>>> estimation of the noise covariance and a regularization parameter. This
>>> scaling process changes the output, which is no longer strictly measured in
>>> physical units (like current density) but is reported in a.u. or normalized
>>> quantity. sLORETA and eLORETA operate under a similar concept of weighted
>>> or standardized normalization (I am simplifying!).
>>>
>>> 2.  I think so, but you must calculate the PSD on the estimated source
>>> time series. For distributed solutions the data is contained in the
>>> source.avg.mom field, not source.avg.pow, if I remember correctly.
>>> You need to restructure the source.avg.mom field so that FieldTrip
>>> treats each source location as a separate "channel" before running
>>> ft_freqanalysis.
>>> Something like:
>>>
>>> cfg = [];
>>> cfg.method = 'mtmfft'; % or whatever
>>> cfg.output = 'pow';
>>> cfg.foi = 0.5:0.5:40; % freqs
>>> freq_source = ft_freqanalysis(cfg, source_data);
>>>
>>> The resulting PSD may look "weird" compared to sensor-level data because
>>> the spatial filter (source method) affects the spectral profile of the
>>> noise and signal.
>>> Ciao,
>>>
>>> Ivano
>>>
>>> ---
>>>
>>> *A. Ivano Triggiani, Ph.D.*
>>>
>>>
>>> ________________________________________________
>>>
>>>
>>>
>>> On Tue, Dec 16, 2025 at 11:55 AM Fabio Strappazzon via fieldtrip <
>>> fieldtrip at science.ru.nl> wrote:
>>>
>>>> Dear all,
>>>>
>>>> I'm currently using wMNE as inverse operator.
>>>> I would like to know two things:
>>>>
>>>> 1) What are the units of measure of source reconstructed activity? I
>>>> see that many papers report them as arbitrary units (a.u.) but I would like
>>>> to know more why is that the case.
>>>>
>>>> 2) Would it be possible to still apply the FieldTrip functions for
>>>> calculating PSDs (ft_freqanalysis) on outputs from source recontructed data
>>>> with distributed apporaches (like MNE) or there are some specific functions
>>>> for those kind of data? If so, on which outputs are calculated: on the
>>>> source.avg.mom or the source.avg.pow?
>>>>
>>>> Many thanks,
>>>>
>>>> --
>>>> *Strappazzon Fabio, *
>>>> *PhD Student at ITAB (Institute for Advanced Biomedical Technologies) -
>>>> Chieti*
>>>> _______________________________________________
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>>>>
>>>
>>
>> --
>> *Strappazzon Fabio, *
>> *PhD Student at ITAB (Institute for Advanced Biomedical Technologies) -
>> Chieti*
>>
>
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