[FieldTrip] Questions on Functional Connectivity results using debiased wPLI
Schoffelen, J.M. (Jan Mathijs)
janmathijs.schoffelen at donders.ru.nl
Thu Sep 23 09:43:57 CEST 2021
Hi Sergio,
As an addition to the previous e-mail: please define cfg.latency as a 2-element vector with a begin and end point, not as a multiple-element vector, as per the documentation.
Best wishes,
Jan-Mathijs
On 23 Sep 2021, at 03:08, SERGIO OSORIO GALEANO via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:
Dear Jan,
Here's a follow up question on this thread.
I understand now that 'mtmfft' provides an estimate of the spectrum using the whole trial. I also understand that if I want to estimate the wPLI for a specific time window within my trial, I should either 1) use a time-resolved method when calling ft_freqanalysis (e.g. wavelet) or 2) call ft_selectdata prior to using 'mtmfft' in ft_freqanalysis.
Because it is less computationally demanding, I tried the second option. However, I've noticed that ft_freqanalysis throws an error if I try to use ft_selectdata with a time window shorter than one second. After inspecting the output structure of ft_selectdata, it seems as though the function performs an average on the second dimension for the first trial only. When I use a latency over a second, this does not happen and all trials have the same dimensions. My question is: am I doing anything wrong or have I again made a wrong assumption while implementing this pipeline? Is there any reason for this strange output? See code snippet below. Thanks a lot in advance!
cfg = [ ];
data = ft_preprocessing(cfg,rwdata);
% resample data
cfg = [];
cfg.resamplefs = 250;
data = ft_resampledata(cfg, data);
data =
struct with fields:
fsample: 250
trial: {1×117 cell}
time: {1×117 cell}
label: {100×1 cell}
cfg: [1×1 struct]
% select the portion of the data I want to compute the wPLI for
cfg = [ ];
cfg.latency = .15:.25; <<<<<<<<<<<<<< if I use 0:1 or 1:1.5, ft_freqanaylisis runs without any problem, but if I use any other latency within 1 second it doesn't work.
data = ft_selectdata(cfg,data);
% here's the output structure
data =
struct with fields:
fsample: 250
trial: {1×117 cell}
time: {1×117 cell}
label: {100×1 cell}
cfg: [1×1 struct]
data.trial
ans =
1×117 cell array
Columns 1 through 9
{100×1 double} {100×1251 double} {100×1251 double} % averaged first trial in the 2nd dimension instead of selecting the time interval of interest
data.time
ans =
1×117 cell array
Columns 1 through 10
{[0.1480]} {1×1251 double} {1×1251 double}
% Now call the ft_freqanalysis function
cfg = [ ];
cfg.output = 'fourier';
cfg.method = 'mtmfft';
cfg.taper = 'dpss';
cfg.foi = linspace(1,31,60);
cfg.tapsmofrq = 4;
tf_data = ft_freqanalysis(cfg,data);
Error using dpss>parseinputs (line 308)
Time-bandwidth product NW must be a positive number.
Error in dpss (line 62)
[method,k,Ni,traceFlag,N,NW] = parseinputs(N,NW,varargin{:});
Error in ft_specest_mtmfft>double_dpss (line 362)
tap = dpss(double(a), double(b), varargin{:});
Error in ft_specest_mtmfft (line 151)
tap = double_dpss(ndatsample,ndatsample*(tapsmofrq./fsample))';
Error in ft_freqanalysis (line 563)
[spectrum,ntaper,foi] = ft_specest_mtmfft(dat, time, 'taper', cfg.taper, options{:}, 'feedback', fbopt);
Error in Connectivity_wPLI (line 68)
tf_data = ft_freqanalysis(cfg,data);
All best,
Sergio.
El mié, 15 sept 2021 a las 15:09, SERGIO OSORIO GALEANO (<srosorio at uc.cl<mailto:srosorio at uc.cl>>) escribió:
Yes, you made a mistake in the (assumptions underlying) the implementation: the cfg.toi that you supply before ft_freqanalysis is not going to have any effect if you use ‘mtmfft’ as a method, since this method just provides a single estimate of the spectrum using the whole ’trial’ for the estimation.
Oh, that makes perfect sense. Cheers Jan! Really appreciate it.
Sergio.
El mié, 15 sept 2021 a las 14:29, Schoffelen, J.M. (Jan Mathijs) via fieldtrip (<fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>>) escribió:
Hi Sergio,
>
> 1) Regardless of whether I use my full time window of interest (0-1.5 s) or whether I estimate wPLI for two separate shorter time windows (0-.7 s and .7-1.5 s), the results are always identical to one another. Is this normal behaviour in wPLI analyses or is there something potentially wrong with how I've implemented it?
Yes, you made a mistake in the (assumptions underlying) the implementation: the cfg.toi that you supply before ft_freqanalysis is not going to have any effect if you use ‘mtmfft’ as a method, since this method just provides a single estimate of the spectrum using the whole ’trial’ for the estimation.
> 2) I notice that wPLI values are way lower for low-frequencies (4-7hz) than for higher-frequencies (8-12hz and 15-30hz). While this could be a real effect associated with my task, the fact that this result is consistent across different conditions makes me wonder whether I've done something wrong in the ft_freqanalysis configuration.
I think that this is just a property of the data.
Best wishes,
Jan-Mathijs
>
> Thanks a lot in advance for any help anyone can provide!
>
> -----------
>
> cfg = [ ];
> data = ft_preprocessing(cfg,rwdata);
>
> %resample data
> cfg = [ ];
> cfg.resamplefs = 250;
> data = ft_resampledata(cfg, data);
>
> data =
> struct with fields:
>
> fsample: 250
> trial: {1×117 cell}
> time: {1×117 cell}
> label: {100×1 cell}
> cfg: [1×1 struct]
>
> % next, call the ft_freqanalysis function in our source data
> cfg = [ ];
> cfg.output = 'fourier';
> cfg.method = 'mtmfft';
> cfg.taper = 'dpss';
> cfg.foi = linspace(4,30,30);
> cfg.tapsmofrq = 4;
> cfg.toi = 0:.02:1.5; % try 0:.02:.7 and .7:.02:1.5
> tf_data = ft_freqanalysis(cfg,data);
>
> tf_data =
> struct with fields:
>
> label: {100×1 cell}
> dimord: 'rpttap_chan_freq'
> freq: [1×30 double]
> fourierspctrm: [4563×100×30 double]
> cumsumcnt: [117×1 double]
> cumtapcnt: [117×1 double]
> cfg: [1×1 struct]
>
> % estimate wPLI values
> cfg = [ ];
> cfg.method = 'wpli_debiased';
> connect_data = ft_connectivityanalysis(cfg,tf_data);
>
> connect_data =
> struct with fields:
>
> label: {100×1 cell}
> dimord: 'chan_chan_freq'
> wpli_debiasedspctrm: [100×100×30 double]
> freq: [1×30 double]
> cfg: [1×1 struct]
>
> Best,
>
> Sergio.
>
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