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ft_connectivity_ppc.m
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Wed, May 28, 03:53

ft_connectivity_ppc.m
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function [c, v, n] = ft_connectivity_ppc(input, varargin)
% FT_CONNECTIVITY_PPC computes pairwise phase consistency or weighted
% pairwise phase consistency from a data-matrix containing a cross-spectral
% density. It implements the method described in: Vinck M, van Wingerden M,
% Womelsdorf T, Fries P, Pennartz CM. The pairwise phase consistency: a
% bias-free measure of rhythmic neuronal synchronization. Neuroimage. 2010
% May 15;51(1):112-22
%
% Use as
% [c, v, n] = ft_connectivity_ppc(input, varargin)
%
% The input data input should be organized as:
%
% Repetitions x Channel x Channel (x Frequency) (x Time)
%
% or
%
% Repetitions x Channelcombination (x Frequency) (x Time)
%
% The first dimension should contain repetitions and should not contain an
% average already. Also, it should not consist of leave one out averages.
%
% Additional input arguments come as key-value pairs:
%
% feedback 'none', 'text', 'textbar' type of feedback showing progress of
% computation
% weighted 1 (or true) or 0 (or false), we compute unweighted ppc or
% weighted ppc, the weighting is according to the magnitude of
% the cross-spectrum
%
% The output c contains the ppc, v is a leave-one-out variance estimate
% which is only computed if dojack = 1,and n is the number of repetitions
% in the input data.
%
% See also FT_CONNECTIVITYANALYSIS
% Copyright (C) 2011, Martin Vinck
%
% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
% for the documentation and details.
%
% FieldTrip is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
%
% FieldTrip is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with FieldTrip. If not, see <http://www.gnu.org/licenses/>.
%
% $Id$
feedback = ft_getopt(varargin, 'feedback', 'none');
weighted = ft_getopt(varargin, 'weighted');
dojack = ft_getopt(varargin, 'dojack');
siz = size(input);
n = siz(1);
ft_progress('init', feedback, 'computing metric...');
if n>1
if ~weighted
input = input./abs(input); % normalize the crosspectrum
outsum = nansum(input); % compute the sum; this is 1 x size(2:end)
c = (outsum.*conj(outsum) - n)./(n*(n-1)); % do the pairwise thing in a handy way
else
outsum = nansum(input); % normalization of the WPLI
outssq = nansum(input.*conj(input));
outsumw = nansum(abs(input));
c = (outsum.*conj(outsum) - outssq)./(outsumw.*conj(outsumw) - outssq); % do the pairwise thing in a handy way
end
c = reshape(c,siz(2:end)); % remove the first singular dimension
else
c = NaN(siz(2:end)); % for one observation, we should return NaNs
ft_warning('ft_connectivity_ppc:nTrials', 'computation ppc requires >1 trial, returning NaNs')
end
[leave1outsum, leave1outssq] = deal(0);
if dojack && n>2 % n needs to be larger than 2 to get a meaningful variance
for k = 1:n
% this code works with both formats of input, also if it is 5-D
s = outsum - input(k,:,:,:,:,:,:); % index up to 7-D, this also works for 5-D then.
if ~weighted
num = s.*conj(s) - (n-2);
denom = (n-1)*(n-2);
else
sq = outssq - input(k,:,:,:,:,:,:).*conj(input(k,:,:,:,:,:,:));
sw = outsumw - abs(input(k,:,:,:,:,:,:));
num = s.*conj(s) - sq;
denom = sw.*conj(sw) - sq;
end
leave1outsum = leave1outsum + num./denom;
leave1outssq = leave1outssq + (num./denom).^2;
end
% compute the sem here
v = (n-1).^2*(leave1outssq - (leave1outsum.^2)./n)./(n - 1); % 11.5 efron, sqrt and 1/n done in ft_connectivityanalysis
v = reshape(v,siz(2:end)); % remove the first singular dimension
elseif dojack && n<=2
v = NaN(siz(2:end));
else
v = [];
end
ft_progress('close');

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