run meeg timefreq measuresΒΆ

Matlab output: run_meeg_timefreq_measures

%% MEEG time-frequency searchlight
%
% This example shows MVPA analyses performed on MEEG data, using a
% searchlight across the time, frequency and channel dimensions
%
% The input dataset involved a paradigm with electrical median nerve
% stimulation for durations of 2s at 20Hz.
%
% The code presented here can be adapted for other MEEG analyses, but
% there are a few potential caveats:
% * assignment of targets (labels of conditions) is based here on
%   stimulation periods versus pre-stimulation periods. In typical
%   analyses the targets should be based on different trial conditions, for
%   example as set a FieldTrip .trialinfo field.
% * assignment of chunks (parts of the data that are assumed to be
%   independent) is based on a trial-by-trial basis. For cross-validation,
%   the number of chunks is reduced to two to speed up the analysis.
% * the time window used for analyses is rather small. This means that in
%   particular for time-freq analysis a lot of data is missing, especially
%   for early and late timepoints in the lower frequency bands. For typical
%   analyses it may be preferred to use a wider time window.
% * the current examples do not perform baseline corrections or signal
%   normalizations, which may reduce discriminatory power.
%
% Note: running this code requires FieldTrip.
%
% #   For CoSMoMVPA's copyright information and license terms,   #
% #   see the COPYING file distributed with CoSMoMVPA.           #


%% get timelock data in CoSMoMVPA format

% set configuration
config=cosmo_config();
data_path=fullfile(config.tutorial_data_path,'meg_20hz');

% show dataset information
readme_fn=fullfile(data_path,'README');
cosmo_type(readme_fn);

% reset citation list
cosmo_check_external('-tic');

% load data
data_fn=fullfile(data_path,'subj102_B01_20Hz_timefreq.mat');
data_tf=load(data_fn);

% convert to cosmomvpa struct
ds=cosmo_meeg_dataset(data_tf);

% set the target (trial condition)
% here, 1=pre-stimulus, 2=peri-stimulus
ds.sa.targets=ds.sa.trialinfo(:,1);

% set the chunks (independent measurements)
% in this dataset, the first half of the samples (in order)
% are the post-trials;
% the second half the pre-trials
ds.sa.chunks=[(1:145) (1:145)]';

% just to check everything is ok
cosmo_check_dataset(ds);

% get rid of features with at least one NaN value across samples
fa_nan_mask=sum(isnan(ds.samples),1)>0;
fprintf('%d / %d features have NaN\n', ...
            sum(fa_nan_mask), numel(fa_nan_mask));
ds=cosmo_slice(ds, ~fa_nan_mask, 2);



% Define a channel neighborhood uses meg_combined_from_planar, which means
% that input are planar channels but the output has
% combined-planar channels. Note that with EEG data there is no need to set
% the chan_type, as there is only a single type.
chan_type='meg_combined_from_planar';
chan_count=10;        % use 10 channel locations (relative to the combined
                      % planar channels)
                      % as we use meg_combined_from_planar there are
                      % 20 channels in each searchlight because
                      % gradiometers are paired

% Use cosmo_meeg_chan_neighborhood to define a channel neighborhood,
% with 'count' set to chan_count, and 'chantype' set to chan_type.
% Assign the result to chan_nbrhood. How many searchlight centers are in
% the neighborhood?
chan_nbrhood=cosmo_meeg_chan_neighborhood(ds, 'count', chan_count, ...
                                              'chantype', chan_type);
fprintf('There are %d channel neighborhood centers\n',...
            numel(chan_nbrhood.neighbors));

% Define the frequency neighborhood using 9 time bins
freq_radius=0; % 4*2+1=9 freq bins


% Use cosmo_interval_neighborhood to define the frequency neighborhood.
% Assign the result to a variable 'freq_nbrhood'
% How many searchlight centers are in the neighborhood?
freq_nbrhood=cosmo_interval_neighborhood(ds,'freq',...
                                            'radius',freq_radius);
fprintf('There are %d frequency neighborhood centers\n',...
            numel(freq_nbrhood.neighbors));

% Define the temporal neighborhood using 5 time bins

time_radius=2; % 2*2+1=5 time bines
% Use cosmo_interval_neighborhood to define the temporal neighborhood.
% Assign the result to a variable 'time_nbrhood'
% How many searchlight centers are in the neighborhood?
time_nbrhood=cosmo_interval_neighborhood(ds,'time',...
                                            'radius',time_radius);
fprintf('There are %d temporal neighborhood centers\n',...
            numel(time_nbrhood.neighbors));



% cross the three neighborhoods to get a chan-freq-time neighborhood,
% using cosmo_cross_neighborhood
% How many searchlight centers are in the crossed neighborhood?

nbrhood=cosmo_cross_neighborhood(ds,{chan_nbrhood,...
                                        freq_nbrhood,...
                                        time_nbrhood});

% Count how many features there are, on average, in each neighborhood,
% and store the results in a variable 'nbrhood_nfeatures'. Then print its
% average and standard deviation

nbrhood_nfeatures=cellfun(@numel,nbrhood.neighbors);
fprintf('Features have on average %.1f +/- %.1f neighbors\n', ...
            mean(nbrhood_nfeatures), std(nbrhood_nfeatures));

% divide .sa.chunks in ds into four chunks using cosmo_chunkize

nfolds=4;
ds.sa.chunks=cosmo_chunkize(ds,nfolds);

% Define partitions using cosmo_nfold_partitioner, and use
% cosmo_balance_partitions afterwards. Assign the result to a variable
% 'partitions'
partitions=cosmo_nfold_partitioner(ds);
partitions=cosmo_balance_partitions(partitions,ds);

% Set the measure arguments
measure_args=struct();
measure_args.partitions=partitions;

%% run searchlight

% only keep features with at least 10 neighbors
% (some have zero neighbors - in particular, those with low frequencies
% early or late in time)
center_ids=find(nbrhood_nfeatures>10);

% instead of using the cosmo_searchlight function, use the faster
% cosmo_naive_bayes_classifier_searchlight.
% As input it takes a dataset, neighborhood, and measure_args.
% Also provide it with the 'center_ids',center_ids argument as well
% to avoid computing results for features without neighbors.

% It may take a while before results for the first fold are computed
result_ds=cosmo_naive_bayes_classifier_searchlight(ds,...
                                        nbrhood,measure_args,...
                                        'center_ids',center_ids);
%% visualize results

% deduce layout from output
layout=cosmo_meeg_find_layout(result_ds);
fprintf('The output uses layout %s\n', layout.name);

% map to FT struct for visualization
tf_map=cosmo_map2meeg(result_ds);

% show figure
figure()
cfg = [];
if cosmo_wtf('is_octave')
    % GNU Octave does not show data when labels are shown
    cfg.interactive='no';
    cfg.showlabels='no';
else
    % Matlab supports interactive viewing and labels
    cfg.interactive = 'yes';
    cfg.showlabels = 'yes';
end
cfg.zlim=[0 1];
cfg.layout       = layout;
ft_multiplotTFR(cfg, tf_map);

% Show citation information
cosmo_check_external('-cite');