[FieldTrip] Calculate epoched time-series in source space (ROI)

Thu Jun 10 11:26:18 CEST 2021

Dear Myrto,

I think that you first need to get clear on what typo of source reconstruction algorithm you’d need.
I recommend not to use the rawtrial option (which only applies to beamformers anyhow as far as I know).
The strategy would be to call ft_sourceanalysisi with cfg.<method>.keepfilter = ‘yes’;
The result of the call to ft_sourceanalysis can then be used in ft_virtualchannel, to obtain single epoch signals.

Best wishes,
Jan-Mathijs

On 9 Jun 2021, at 18:57, Myrto Mantziara via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:

Dear Jan-Mathijs,

Thank you for your suggestion - it is very helpful. Your description of it as 'virtual channels' seems to express what we want to do. Before I move on to try this, I wanted to make sure that I can do the source analysis trial by trial. Should be enough if I just choose cfg.rawtrial = 'yes' ? Since the data input in the ft_sourceanalysis are as obtained from ft_timelockanalysis, will ft_sourceanalysis use the 'avg' field of the time-locked data struct or the trial x channel x time data from the 'trial' field (to get this I have chosen cfg.keeptrials = 'yes' in ft_timelockanalysis)?

Regards,
Myrto

--------------------
Myrto Mantziara
PhD Candidate
School of Psychology
Bangor University
United Kingdom
Email: m.mantziara at bangor.ac.uk<mailto:m.mantziara at bangor.ac.uk>
Lab Website: sites.google.com/site/kkornysheva/<http://sites.google.com/site/kkornysheva/>
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________________________________
From: fieldtrip <fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl>> on behalf of Schoffelen, J.M. (Jan Mathijs) via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>>
Sent: 09 June 2021 16:07
To: FieldTrip discussion list <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>>
Cc: Schoffelen, J.M. (Jan Mathijs) <jan.schoffelen at donders.ru.nl<mailto:jan.schoffelen at donders.ru.nl>>
Subject: Re: [FieldTrip] Calculate epoched time-series in source space (ROI)

Dear Myrto,

I think that what you ask is ‘how do I create a (set of) virtual channel(s)?’

There is no dedicated documentation for this  yet. First of all, I think that you need to look into source reconstruction. After computing the forward model (a.k.a. as the leadfields) you need to use this in order to ’source reconstruct’ the channel level data, using some sourceanalysis method. More precisely, you need to compute an 'inverse operator’ which can be used to left multiply your sensor data with, in order to obtain single epoch time course of the ‘virtual channels’.

The virtual channels can be computed using the ft_virtualchannel function. Yet, in order to be able to use this, you need to use ft_sourceanalysis first.

Best wishes,
Jan-Mathijs

On 9 Jun 2021, at 16:38, Myrto Mantziara via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:

Dear Fieldtrip Team,

I would like to extract epoched EEG data from dipole sources in a Region of Interest (ROI). For the forward solution in the source analysis, I reconstructed the sources using the standard BEM headmodel (found in the Fieldtrip directory: fieldtrip-20160814\template\headmodel\standard_bem.mat) and computed the leadfield. Now I would like to apply the dipole leadfield weights to extract epoched time-series from dipoles of interest, e.g., all dipoles located in the primary motor cortex. In other words, I would like to examine the epoched data in source space (amplitude for each dipole for MVPA analysis, and time-frequency data averaged across the ROI). Also, we are not sure which leadfield weight to include (dipole orientations).
Last, do you have a function that does such weighting correctly to achieve orthogonalization in the contribution of other sources (e.g., nearby to the ROI sources) in order to increase specificity.
Perhaps there is an example code or other functions which I have not come across.

We would appreciate your help.

Regards,

Myrto Mantziara

--------------------
Myrto Mantziara
PhD Candidate
School of Psychology
Bangor University
United Kingdom
Email: m.mantziara at bangor.ac.uk<mailto:m.mantziara at bangor.ac.uk>
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