[FieldTrip] Questions on Functional Connectivity results using debiased wPLI
SERGIO OSORIO GALEANO
srosorio at uc.cl
Thu Sep 23 15:33:55 CEST 2021
Dear Jan and anyone reading this thread in the future,
Sorry, I hadn't seen this email before. Actually, this solved the issue. In
conclusion, specifying the parameter in an unconventional way caused the
error. I also noticed that shorter latencies will require accommodating the
smoothing parameter.
Thank you very much again!
*Sergio A. Osorio*
Laboratory for Cognitive and Evolutionary Neuroscience
Center for Medical Research - Faculty of Medicine
Pontificia Universidad Católica de Chile
El jue, 23 sept 2021 a las 5:17, Schoffelen, J.M. (Jan Mathijs) via
fieldtrip (<fieldtrip at science.ru.nl>) escribió:
> 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> 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>)
> 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>) 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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