[FieldTrip] About source reconstruction outputs

[Domenica Veniero (staff)]

[like]  Domenica Veniero (staff) reacted to your message:
________________________________
From: fieldtrip <fieldtrip-bounces at science.ru.nl> on behalf of Fabio Strappazzon via fieldtrip <fieldtrip at science.ru.nl>
Sent: Wednesday, December 17, 2025 11:50:35 AM
To: ivano triggiani <ivanotriggiani at gmail.com>
Cc: Fabio Strappazzon <fab.strappaz at gmail.com>; FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] About source reconstruction outputs

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<mailto: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<mailto: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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