ICA with Fieldtrip (1)

Independant Component Analysis — Computing

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First, you have to got tell Matlab where your data and your scripts are.

Then, you should also load subjects list (it is a function, that you have to create — hard-code — yourself).

subjects_list = suj();

We will also calculate the number of subject involved in the analysis (for the following analysis loop)

nb_subjects = size(subjects_list,1);

The loop that perform the ICA analysis on all subjects:

for s = 1:nb_subjects;
do_icaeog(datpath, subjects_list (s,:));
end; % for s

To have an exemple on how to look at its results: see Independant Component Analysis — Visualization

The function do_icaeog.m :

function comp = do_icaeog(datpath, name_file)
%%% perform an Independant Component Analysis on MEG raw data
%%% files list
filist = dir([datpath name_file '*.ds']);
%%% who are these files
disp(' '); disp(' ') ;
fprintf('              **** got datasets from %s ****', name_file)
disp('- these files are: ');  disp(' ') ;
fprintf('             %s  ', filist.name_file); disp(' '); disp(' ') ;
%%% load data
for f = 1:length(filist)
    rawfiles= [datpath filist(f).name_file];
%%% load and preprocess the data
    cfg = [];
    %%%
    cfg.channel         = 'MEG';
    cfg.dftfilter       = 'yes'; 
    cfg.dftfreq         = [50 100 150];
    cfg.padding         = 2;
    % cfg.headerfile
    cfg.bpfilter        = 'yes';
    cfg.bpfreq          = [1 150];
    %%%
    cfg.dataset         = rawfiles;
    cfg.continuous      = 'yes';
    cfg.demean          = 'no'; %%%%
    
    cleandata = ft_preprocessing(cfg); clear rawfiles;
    
    
%%% data resampling for speed
    cfg = []; 
    cfg.resemplefs = 300;
    cfg.detrend = 'no';
    rsdata = ft_resampledata(cfg,cleandata); 
    clear cleandata;
if exist ([datpath 'ica'], 'dir') == 0
    mkdir([datpath 'ica']);
end; % if exist
icapath = [datpath 'ica/'];
%%% raw resampled data are needed for further data analysis 
save ([icapath name_file '_rsdata_block' num2str(f)], 'rsdata');

%%% the ICA itself
    cfg = [];
    cfg.method = 'runica';
    comp = ft_componentanalysis(cfg, rsdata); clear rsdata;
save ([icapath name_file '_comp_block' num2str(f)], 'comp'); clear comp;
   
end; % for f
%%% the end

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