Analyze MIMIC III waveform data directly in Matlab

I would like to analyze MIMIC III waveform data (mainly PPG and ABP) directly in Matlab on a MacOS without going through Google or AWS database queries. Has anyone done this? Can you advise me on the best way?

Thanks

Ram

[Douaa]

hey, did you get the data? could you please show me how did you get it? thanks in advance

Answer 1

[William Rose]

@Ram Krishnan,

After you reigtser on the physionet site, you may use the package here

https://archive.physionet.org/physiotools/matlab/wfdb-app-matlab/

You should also check out the use of "wget" to download files from the MIMIC-III database, as described here:

https://physionet.org/content/mimic3wdb/1.0/30/3000003/#files-panel

(Scroll down to wget, or search the page for wget.)

wget is not part of Mac OS, but you can get it. Google "wget for Mac". I am not a Mac person.

[Ram Krishnan]

William,

That is hugely helpful as all the exploring I did on Matlab's Help site and on Google were unproductive. I'll try both tools out.

Thanks

Ram

[William Rose]

@Ram Krishnan, you're welcome. Good luck with your research.

Answer 2

[Ram Krishnan]

clc;clear;close all;

fileDir = '/myMimicDir/';

recList = append(fileDir,'mimic3wdbRecordsWithPpgANDbp.txt');

fileID = fopen(recList);

numRecs = 10; % number of data records to read and write into excel

numSamples = 1000000; % number of samples to read and write in each record

for i = 1:numRecs

wdbRec(i) = textscan(fileID,'%s \n');

% wdbRec{i}

end

fclose(fileID);

for i = 1:numRecs

[fileNameTemp,~,~] = wfdbdesc(char(wdbRec{i}));

fileName = struct2cell(fileNameTemp);

[~,~,numVar] = size(fileName);

for j=1:numVar

varName = fileName(9,1,j);

if contains(varName,'PLETH')

ppgCol = j;

elseif contains(varName,'ABP')

abpCol = j;

end

end

recName = cell2mat(wdbRec{1,i});

fprintf('Record number %d \n',i);

fprintf('Now in rdsamp.. \n')

[signal,Fs,tm]=rdsamp(recName,[ppgCol abpCol],numSamples);

writeFileDir = '/myMimicDir/PPG-ABP dataset created by ReadMimic3wdbFileList_092324/';

recLabel = recName(end-23:end); % use last 23 char of recName to create a spreadsheet name

writeFileName = append(writeFileDir,recLabel);

excelFileName = append(writeFileName,'.xlsx');

fprintf('Now in writematrix..\n')

writematrix(signal,excelFileName);

%%% plot for visualizing signals

% figure

% plot(tm(5000:10000),signal(5000:10000,1)); % first 5000 samples may be noise

% figure

% plot(tm(5000:10000),signal(5000:10000,2))

end