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reference:ft_connectivityanalysis [2018/08/23 14:43] (current)
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 +Note that this reference documentation is identical to the help that is displayed in MATLAB when you type "help ft_connectivityanalysis"​.
 +  <a href=/​reference/​ft_connectivityanalysis><​font color=green>​FT_CONNECTIVITYANALYSIS</​font></​a>​ computes various measures of connectivity between
 +  MEG/EEG channels or between source-level signals.
 +  Use as
 +    stat = ft_connectivityanalysis(cfg,​ data)
 +    stat = ft_connectivityanalysis(cfg,​ timelock)
 +    stat = ft_connectivityanalysis(cfg,​ freq)
 +    stat = ft_connectivityanalysis(cfg,​ source)
 +  where the first input argument is a configuration structure (see below)
 +  and the second argument is the output of <a href=/​reference/​ft_preprocessing><​font color=green>​FT_PREPROCESSING</​font></​a>,​
 +  FT_TIMELOCKANLAYSIS,​ <a href=/​reference/​ft_freqanalysis><​font color=green>​FT_FREQANALYSIS</​font></​a>,​ <a href=/​reference/​ft_mvaranalysis><​font color=green>​FT_MVARANALYSIS</​font></​a>​ or <a href=/​reference/​ft_sourceanalysis><​font color=green>​FT_SOURCEANALYSIS</​font></​a>​.
 +  The different connectivity metrics are supported only for specific
 +  datatypes (see below).
 +  The configuration structure has to contain
 +    cfg.method ​ =  string, can be
 +      '​amplcorr', ​ amplitude correlation,​ support for freq and source data
 +      '​coh', ​      ​coherence,​ support for freq, freqmvar and source data.
 +                   For partial coherence also specify cfg.partchannel,​ see below.
 +                   For imaginary part of coherency or coherency also specify
 +                   ​cfg.complex,​ see below.
 +      '​csd', ​      ​cross-spectral density matrix, can also calculate partial
 +                   csds - if cfg.partchannel is specified, support for freq
 +                   and freqmvar data
 +      '​dtf', ​      ​directed transfer function, support for freq and
 +                   ​freqmvar data
 +      '​granger', ​  ​granger causality, support for freq and freqmvar data
 +      '​pdc', ​      ​partial directed coherence, support for freq and
 +                   ​freqmvar data
 +      '​plv', ​      ​phase-locking value, support for freq and freqmvar data
 +      '​powcorr', ​  power correlation,​ support for freq and source data
 +      '​powcorr_ortho',​ power correlation with single trial
 +                   ​orthogonalisation,​ support for source data
 +      '​ppc' ​       pairwise phase consistency
 +      '​psi', ​      ​phaseslope index, support for freq and freqmvar data
 +      '​wpli', ​     weighted phase lag index (signed one,
 +                   still have to take absolute value to get indication of
 +                   ​strength of interaction. Note: measure has positive
 +                   bias. Use wpli_debiased to avoid this.
 +      '​wpli_debiased' ​ debiased weighted phase lag index
 +                   ​(estimates squared wpli)
 +      '​wppc' ​      ​weighted pairwise phase consistency
 +      '​corr' ​      ​Pearson correlation,​ support for timelock or raw data
 +  Additional configuration options are
 +    cfg.channel ​   = Nx1 cell-array containing a list of channels which are
 +      used for the subsequent computations. This only has an effect when
 +      the input data is univariate. See <a href=/​reference/​ft_channelselection><​font color=green>​FT_CHANNELSELECTION</​font></​a>​
 +    cfg.channelcmb = Nx2 cell-array containing the channel combinations on
 +      which to compute the connectivity. This only has an effect when the
 +      input data is univariate. See <a href=/​reference/​ft_channelcombination><​font color=green>​FT_CHANNELCOMBINATION</​font></​a>​
 +    cfg.trials ​    = Nx1 vector specifying which trials to include for the
 +      computation. This only has an effect when the input data contains
 +      repetitions.
 +    cfg.feedback ​  = string, specifying the feedback presented to the user.
 +      Default is '​none'​. See <a href=/​reference/​ft_progress><​font color=green>​FT_PROGRESS</​font></​a>​
 +  For specific methods the cfg can also contain
 +    cfg.partchannel = cell-array containing a list of channels that need to
 +      be partialized out, support for method '​coh',​ '​csd',​ '​plv'​
 +    cfg.complex ​    = '​abs'​ (default), '​angle',​ '​complex',​ '​imag',​ '​real',​
 +      '​-logabs',​ support for method '​coh',​ '​csd',​ '​plv'​
 +    cfg.removemean ​ = '​yes'​ (default), or '​no',​ support for method
 +      '​powcorr'​ and '​amplcorr'​.
 +    cfg.bandwidth ​  = scalar, (default = Rayleigh frequency), needed for
 + ​ '​psi',​ half-bandwidth of the integration across frequencies (in Hz)
 +  To facilitate data-handling and distributed computing you can use
 +    cfg.inputfile ​  ​= ​ ...
 +    cfg.outputfile ​ =  ...
 +  If you specify one of these (or both) the input data will be read from a *.mat
 +  file on disk and/or the output data will be written to a *.mat file. These mat
 +  files should contain only a single variable, corresponding with the
 +  input/​output structure.
 +  See also <a href=/​reference/​ft_preprocessing><​font color=green>​FT_PREPROCESSING</​font></​a>,​ <a href=/​reference/​ft_timelockanalysis><​font color=green>​FT_TIMELOCKANALYSIS</​font></​a>,​ <a href=/​reference/​ft_freqanalysis><​font color=green>​FT_FREQANALYSIS</​font></​a>,​
 +  <a href=/​reference/​ft_mvaranalysis><​font color=green>​FT_MVARANALYSIS</​font></​a>,​ <a href=/​reference/​ft_sourceanalysis><​font color=green>​FT_SOURCEANALYSIS</​font></​a>,​ <a href=/​reference/​ft_networkanalysis><​font color=green>​FT_NETWORKANALYSIS</​font></​a>​.
 +  For the implemented methods, see also <a href=/​reference/​ft_connectivity_corr><​font color=green>​FT_CONNECTIVITY_CORR</​font></​a>,​
 +  <a href=/​reference/​ft_connectivity_granger><​font color=green>​FT_CONNECTIVITY_GRANGER</​font></​a>,​ <a href=/​reference/​ft_connectivity_ppc><​font color=green>​FT_CONNECTIVITY_PPC</​font></​a>,​ <a href=/​reference/​ft_connectivity_wpli><​font color=green>​FT_CONNECTIVITY_WPLI</​font></​a>,​
 +  <a href=/​reference/​ft_connectivity_pdc><​font color=green>​FT_CONNECTIVITY_PDC</​font></​a>,​ <a href=/​reference/​ft_connectivity_dtf><​font color=green>​FT_CONNECTIVITY_DTF</​font></​a>,​ <a href=/​reference/​ft_connectivity_psi><​font color=green>​FT_CONNECTIVITY_PSI</​font></​a>​