Is there a way to retrieve physiological data from acqknowledge and preprocess them in R?

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I'm trying to retrieve raw physiological data (hand dynanometer) from Acqknowledge to be able to preprocess and analyze them in R (or Matlab) in an automatized way. Is there a way to do that ? I would like to avoid having to copy/paste the data manually from Acknowledge to Excel to read them in R.

Then I would like to apply a filter on the data and retrieve the squeezes of interest in R. Is there a way to do that ?

Any advice is very welcome, thank you in advance!

data-preprocessing data-retrieval r automation
1 Answers

I had a similar problem. The key is the load_acq.m function, you can find it here -> https://github.com/munoztd0/fusy-octave-memories/blob/main/load_acq.m then you can just loop through them and save them as .csv or anything that you can load and work with in R.

As for how to do that I have put together a little routine to do that.

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Create physiological files from AcqKnowledge
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% SETTING THE PATH
path = 'your path here'; %your path here
physiodir   = fullfile(path, '/SOURCE/physio');
outdir = fullfile(path, '/DERIVATIVES/physio');
session = "first" %your session

base = [path 'sub-**_ses-' session '*'];

subj = dir(base); %check all matching subject for this session

addpath([path '/functions']) % load aknowledge functions
%check here https://github.com/munoztd0/fusy-octave-memories/blob/main/load_acq.m

for i=1:length(subj)

cd (physiodir) %go to the folder

subjO = char(subj(i).name);
subjX =  subjO(end-3:end); %remove .mat extension
filename = [subjX '.acq']; %add .acq extension
                

disp (['****** PARTICIPANT: ' subjX ' **** session ' session ' ****' ]);

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% OPEN FILE
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


physio = load_acq(filename); %load and transform acknowledge file

data = physio.data; %or whatever the name is




%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% CREATE AND SAVE THE CHANNEL
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%



cd (outdir) %go to the folder

% save the data as a file text in the participant directory
fid = fopen([subjX ',txt'],'wt');
for ii = 1:length(data)
    fprintf(fid,'%g\t',data(ii));
    fprintf(fid,'\n');
end
fclose(fid);

end

Hope it helps !

user_131588390
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