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MarcusVollmer/HRV

version 1.07 (10 MB) by Marcus Vollmer
A user friendly application for screening and manipulation of ECG data and the analysis of heart rate variability.

67 Downloads

Updated 03 Nov 2020

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# HRVTool v1.07
## Methods for analyzing Heart Rate Variability

The present functions are originally made for Matlab R2016b. Errors may occur using older releases (at least R2014b required). Additional toolboxes are not required to run the basic analysis.
The Image Processing Toolbox is recommended and required to use the 'picker'-functionality.
Importing ECGs out of PDFs requires Matlab start as administrator and the installation of Inkscape (or for Linux: PDFminer and pdf2svg).

**HRV.m** is a Matlab class containing function for analyzing HRV.
**HRVTool.m** contains the code to start the GUI (Graphical User Interface) on Matlab.
**HRVTool.mlappinstall** is the app package which can be installed with Matlab.

Please run HRVTool.m to start the GUI or click on the icon in the App menu of Matlab.
The user interface has been tested on Windows 10, Linux Ubuntu 18.04 and Mac OS 10.15.6.

### Supported file types
- [x] HRM - Polar files
- [x] MAT - Matlab files, structures or workspace variables containing waveforms or RR intervals (in ms)
- [x] TXT - text files containing waveforms or RR intervals (in ms)
- [x] ECG - PhysioNet files (PhysioNet wfdb toolbox required)
- [x] WAV - Hexoskin files
- [x] EDF - European Data Format
- [x] ACQ - BIOPAC data (Source code of Jimmy Shen)
- [x] ISHNE - Holter Standard Format (ECG and annotation data)
- [x] MIBF - Machine Independent Beat file (GE Marquette holter format)
- [x] PDF - ECG-PDFs from Apple Watch and AliveCor devices (Kardia and aliveecg)

Other formats are possible to integrate. Please address your wishes to marcus.vollmer@uni-greifswald.de

Supporting files to load BIOPAC ACQ data (load_acq.m, acq2mat.m) are licensed by Jimmy Shen given the copyright notice LICENSE_ACQ.
Copyright (c) 2009, Jimmy Shen
All other supported files and functions are licensed under the terms of the MIT License (MIT) given in LICENSE and LICENSE_ICONS
Copyright (c) 2015-2020 Marcus Vollmer

27 October 2020

Cite As

Vollmer, Marcus. “HRVTool - an Open-Source Matlab Toolbox for Analyzing Heart Rate Variability.” 2019 Computing in Cardiology Conference (CinC), Computing in Cardiology, 2019, doi:10.22489/cinc.2019.032.

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Vollmer, Marcus. “A Robust, Simple and Reliable Measure of Heart Rate Variability Using Relative RR Intervals.” 2015 Computing in Cardiology Conference (CinC), IEEE, 2015, doi:10.1109/cic.2015.7410984.

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Comments and Ratings (47)

Marcus Vollmer

Dear Charmaine,

The toolbox shows the unfiltered signal, although for heart beat detection kind of band-pass filtering was used. So pre-filtering is not needed/required. But it's up to you, if you would like to load a pre-filtered signal for a better visualization.
There is no need to enter the sampling frequency (Fs) when importing EDF recordings since read_edf.m is computing Fs from the 'number of samples in each data record' and the 'duration of a data record' (in seconds), which are fields in the header of each EDF file.
It is yet not possible to mark complete periods to be excluded from HRV computations. But for short or noisy periods you can mark the R peaks to be ignored (ignore button).

Best,
Marcus

Charmaine Diep

Hi Dr. Vollmer,
I'd like to use this program to analyse HRV during an 8-hour step period. I have a few questions as I'm very green to MATLAB.
My data is in an edf file. Do I need to filter it in any way before importing it into the program, or should it be as unprocessed as possible? At the moment I have it filtered between 0.05 and 100 Hz and a 50 Hz Notch filter. Do I need to mark wake epochs for exclusion?
Where should I enter the sampling frequency as you mentioned in your reply to Lily?
Thank you for creating this program!
Charmaine

Marcus Vollmer

Dear Lily,

These are the steps to take:
1. Make sure that you have installed Inkscape.
2. Download HRVTool and install the Matlab App (help is here: https://de.mathworks.com/discovery/matlab-apps.html)
3. Inside Matlab: Browse to the folder that contains your ECG-PDF.
4. Make sure that Matlab is allowed to write temporary files in this folder.
5. Start HRVTool by clicking on the application icon in the App tab of Matlab.
6. Wait a few seconds for the graphical interface to show the sample recording.
7. To avoid graphics issues: Close the window and start the App again.
8. Click on the folder icon within the GUI and select your ECG-PDF.
9. The ECG will be read from the PDF.
10. Enter the sampling frequency (e.g. 300Hz) and see the results to appear in the GUI.
11. Click on the 'wavefom'-button to see the ECG.
12. Use the buttons below to show the beat locations and intervals.

Cheers,
Marcus

Note: Please use the most recent mlappinstall that you can download here, because unfortunately in an older version path2mat.m was missing.

Lily Wald

Hi Mr. Vollmer,

I'm attempting to upload ECG pdfs from my apple watch, but I'm not as well versed with Matlab and this is a bit over my head. Do you have any advice as to where I need to start?

Marcus Vollmer

The new Version 1.05 is online. What's new: The toolbox is ready to import ECG-PDFs (*.pdf) from Apple Watch and AliveCor Kardia that works on all main OS (MacOS, Windows, Linux/UNIX). It also imports the beat ticks (annotations) that comes with the PDF. All you need is a free installation of Inkscape and you need to start Matlab with administrator rights. For Linux systems a faster solution exist when having the packages pdf2svg and pdfminer installed. For the import of PDFs in batch mode you can use the function read_pdf that converts the pdf to Matlab structure. It's now possible to save the annotations as EDF files and to import signals and annotations from workspace variables. Therefore you need to cancel the import of a file, that automatically directs you to a selection dialog of workspace variables. This is also working when loading annotations. Moreover, the power spectrum was not squared, which is now corrected. The table of HRV parameters contains no Approximate Entropy ApEn.

Tilendra Choudhary

Marcus Vollmer

Dear CdC,

mat files are also supported to import data that contains a single waveform or a sequence of RR intervals in milliseconds or seconds. The mat file should contain an Nx1 vector containing the waveform. The import import of variables directly from the workspace is something I will consider for the next release.
Another way to use workspace variables is the analysis outside the GUI. Here you can make use of batch processing using my HRV matlab class, see:
https://github.com/MarcusVollmer/HRV/blob/master/HRV.m
https://github.com/MarcusVollmer/HRV/blob/master/HRV_sample_batchjob.m
https://github.com/MarcusVollmer/HRV/issues/8

Best,
Marcus

CdC

Thanks for the wonderful tool! Can you provide the format that is required for .mat file waveform data? I have a Matlab array of evenly sampled 100Hz values. How should I save that to be able to read it in using the ’w’ selection? Also, is there a way to run the tool on waveform data in matlab memory and produce output results, rather than running it on file data? Thanks again. I was able to get the matlab data to work if I saved out the matlab array in csv format and then read this into the HRVTool as .txt format file.

CdC

Also, is there a way to run the tool on waveform data in matlab memory and produce output results, rather than running it on file data? Thanks again. I was able to get the matlab data to work if I saved out the matlab array in csv format and then read this into the HRVTool as .txt format file.

santanu sahoo

Marcus Vollmer

Dear Pierre,

I'm sorry that you cannot use this functionality. Here I'm making use of getpts to extract the coordinates when you are clicking. This function comes with the Image Processing Toolbox (IPT).

There are ways to solve your at least your visibility problem without making use of IPT:
You can either add this line to your settings file:
vis = [true true true false false false false];
or you edit line 285 and line 1084 in HRVTool.m.

Concerning your second question about the missing LH/HF measure, I'm not quite sure what you mean with 'extracted variables'. But I assume, that your RR intervals contains NANs, which prevents from the computation of the power spectrum.

Cheers,
Marcus

Pierre Esteves

Particularly, the selection "Remove Artifact not permite to select one artifact with cursor" and it's the same concerning the visualisation ON/OFF and the selection of variables

Pierre Esteves

Hey! Thank you so much for all your help, I really appreciate it. Is it normal that I don't have the same options on the interface as those on your tutorial. When I click on visibility on/off I can't remove the variables to view only the ones I'm interested in.

Then, I wanted to know if it was normal that my extracted variable does not show me the LH, HF and the LH/HF ratio, would it be because I have a free version under 30 days of mathlab?

Last question, how can I make my results after exporting them show the ApEn (Entropy) and all the other possible variables.

Thank you for your attention,

Pierre

Marcus Vollmer

Dear Guillaume,

The tool detects exceptional RR intervals and replaces the value to NaN to exclude this information from HRV calculations.
I recommend not interpolating the normal heart rhythm. By doing so you assume to already know about the heart rate variability pattern, but normally this is, want you are going to assess from the data. FFT-based methods such as HF/LF cannot handle missingness in the interval information without data manipulation and making assumptions as described above. I therefore recommend to use other robust measures for HRV.

Cheers,
Marcus

Guillaume Sans

Hi.
I new in the domain of HRV.
Your tool can correct ectopic beat ? Like linear interpolation or anything else ?
How can i have HF/LF ratio with a NAN ?
Please help me.
Guillaume.
guillaume.sans.1@umontreal.ca

Marcus Vollmer

Dear Eddie,

Welcome in Matlab. To make use of PhysioNet data in Matlab you should download the WFDB Toolbox. Go to https://archive.physionet.org/physiotools/matlab/wfdb-app-matlab/ and follow the instructions as given under 'Quick Start'.

Cheers,
Marcus

Edgar Susiku

i am new to matlab, how do i upload ECG data from Physionet to matlab

please help

es988@live.mdx.ac.uk

Eddie

Paul Beach

sorry - disregard the last post. It started working!

Marcus Vollmer

Dear Gabriel,

I'm not sure, which HR monitor from Polar you are using. But you need an export file containing inter-beat intervals. Please write me an e-mail, if you are still stuck in the analysis.

Best,
Marcus

Gabriel Abdulai

Hello Marcus,
I downloaded some data from my polar heart rate monitor but am unable to process it on your application in matlab. i converted the file to txt but the app keeps asking me if i want to add meta data from hrm-file which I don't. If i clicked no, the process failed. can you please help me out. Thank you.
Gabriel

Marcus Vollmer

Dear Josh,

please save the waveform column separately from the time column as a single columned csv. Import the csv file and fill the dialog window with the file type "waveform" set the sampling frequency to "500" Hz. The time difference is also 0.002 sec for a 512 Hz ECG, so please check the real frequency. Try 'format long' in Matlab.

Best,
Marcus

Josh E. Thamrin

Hi Marcus,

I am trying to get import a CSV file straight from an oscilloscope and have not met with any success so far. The CSV file essentially contains two columns, one with time in 0.002 second increments, and the other with voltage variation from the oscilloscope within a range from -4 to 4 volts. Any ideas as to what I need to do?

Marcus Vollmer

Dear Scott,

First of all please select the appropriate file extension using the the drop down menu, which is a bit hidden on MacOS. Then all files matching the file extension will be listed and can be selected for the import of your data.

Best,
Marcus

Scott Rennie

Hi Marcus.

I have just installed the app into matlab. It doesn't seem to recognize any files, either .mat or .csv as files that can be opened. The demo functions just find. I can't seem to add any of my won data however. Any idea whats up? This is 2016b on a mac

Marcus Vollmer

Dear Dario,

Thank you for your question.
For heart beat detection the toolbox uses a minor changed algorithm which I have published and presented at Computing in Cardiology 2014 (http://www.cinc.org/archives/2014/pdf/0569.pdf). The annotation are made on the basis of the largest range of the input signal in a windowed approach. These annotations can differ from the R peaks e.g. in such cases when the S peaks are deeper than the baseline. If you are interested in the R peak you can easily adjust the calculated annotations while searching for the highest peak nearby, e.g. in the range of +/- 10 samples:
for i=1:size(Ann,1)
[~,locECG] = max(ECG(Ann(i)+[-10:10]));
Ann(i) = Ann(i)+locECG-11;
end

In a future release it planned that you can select from various heart beat detectors and some functions will be added that you can easily adjust the annotations.

Best regards,
Marcus

Dario Geisinger

Hi Marcus and thanks for sharing your work.
I am opening a .mat file with the waveform (fVals) and the HRVTool detects the heart beats and I save the Annotation .mat (Ann). However, If I load fVals.mat with the waveform, plot it and then plot the Ann file, the peaks are not exactly on the waveform peaks (even when the .mat file used is a file created from inside the HRVTool, save sig_waveform). Actually there is sometimes several samples difference.
I want to make sure that the peaks in the waveform signal are indeed the ones in the Ann file and it appears they are not.
Is there any processing that I am missing??
Thanks again for sharing

Dario

Ivan Castillo

Dear Marcus,
I update my version of Matlab R2015a to R2016b and it worked.
Apparently it was a problem of how Matlab handled the "folder" field.

Marcus Vollmer

Dear Ivan,

I'm sorry for that. When starting the app it will search for the installation path to read the example data. On Linux the search for the app path should work with the new commands I introduced recently. Please try the new version 1.02.

Kind regards,
Marcus

Ivan Castillo

Dear Marcus,
I can't open the app, the following error occurs, do you have some suggestion?

Reference to non-existent field 'folder'.

Error in HRVTool (line 28)
AppPath = FileList.folder;

Error in HRVToolApp/startApp (line 59)
eval('HRVTool');

Error in HRVToolApp (line 38)
startApp(obj)

Error in appinstall.internal.runapp>execute (line 79)
out = evalin('caller', [script ';']);

Error in appinstall.internal.runapp1runapp13a (line 58)
outobj = execute(fullfile(appinstalldir, [wrapperfile 'App.m']));

Error in appinstall.internal.runapp>runcorrectversion (line 35)
appobj = runapp13a(appinstalldir);

Error in appinstall.internal.runapp (line 17)
out = runcorrectversion(appmetadata, appentrypoint, appinstalldir);

Jay Alan

Dear Marcus,
Thank you so very much for your inputs. Thanks to it, have been able to use it.
Please keep up the great work!
Regards,
Jay

Marcus Vollmer

Dear Jay,

I'm sorry for that error, which is caused by a false path to the app folder appearing in 'HRV_settings.m'. Please delete that file in your HRVTool app path. HRVTool will then initialize the settings file when restarting HRVTool, reading your personalized app path in Matlab (depending on your operating system).
Another way is the re-installation of HRVTool, which is now updated.

Best,
Marcus

Jay Alan

Jay Alan

Dear Marcus,
Installed HRV App in R2018a on Mac running OS X version 10.9.5 (without any issues)
When I start the App, the window does not load the example; a lot of errors appear on the command window (copy-pasted below). Any pointers would be greatly appreciated. Thanks in advance.
--
> In HRVTool/calc_on (line 1711)
In HRVTool/buttonStart_Callback (line 591)
In HRVTool (line 585)
In HRVToolApp/startApp (line 88)
In HRVToolApp (line 48)
In appinstall.internal.runapp>execute (line 86)
In appinstall.internal.runapp>runapp13a (line 65)
In appinstall.internal.runapp>runcorrectversion (line 44)
In appinstall.internal.runapp (line 19)
Unable to perform assignment with 0 elements on the right-hand side.

Error in HRVTool/buttonStart_Callback (line 596)
FileName = STR{VAL};

Error in HRVTool (line 585)
buttonStart_Callback

Error in HRVToolApp/startApp (line 88)
eval('HRVTool');

Error in HRVToolApp (line 48)
startApp(obj)

Error in appinstall.internal.runapp>execute (line 86)
out = evalin('caller', [script ';']);

Error in appinstall.internal.runapp>runapp13a (line 65)
outobj = execute(fullfile(appinstalldir, [wrapperfile 'App.m']));

Error in appinstall.internal.runapp>runcorrectversion (line 44)
appobj = runapp13a(appinstalldir);

Error in appinstall.internal.runapp (line 19)
runcorrectversion(appmetadata, appentrypoint, addonmetadatadir);

Warning: 'popupmenu' control requires a scalar Value.
Control will not be rendered until all of its parameter values are valid
--

Marcus Vollmer

Dear Varun,
you can save the HRV measures calculated for the global, local and footprint range by clicking on 'File' > 'Save As' and selecting 'mat' or 'csv' as the export format. For a detailed analysis on a segmentwise basis I suggest the use the functions in the HRV.m class.
Best,
Marcus

Varun Sharma

how to export the results?

Marcus Vollmer

Dear Achilleas,

please have a look at my read_edf function:
https://github.com/MarcusVollmer/HRV/blob/master/read_edf.m

There is a way of interactively select on of the channels stored in the edf or to import all signals along with the header information, which are stored in a structure.

Best,
Marcus

Achilleas Pavlou

How do you read edf files?

Soufia dani

could you please share with me your (*.fig) or just explain me how can i regenerate it form file(*.m) becouse really i need it so much.
thanks

Soufia dani

Hi every one i am here to ask you please i wanna knew if are there any possibility to modifiy this app just from it is GUI because i try to add some buton but i cant do it just from GUI i have to come back to the code if i want to change,

Marcus Vollmer

Dear Balu Krishnan,

It sounds to me, that Matlab fails to read the app path to HRVTool. I cannot identify the problem but I assume a reading/writing permission error. Please try to execute the code "HRVTool.m" without reading the app path. To get this running comment lines 21-30 and uncomment line 33. Make sure that you have copied all required files into your working directory and the toolbox should appear.

Best,
Marcus

Balu Krishnan

I tried installing the app in Matlab v2017a and it is taking forever to install the app. When I tried executing the code (HRV_tool), the code does not execute. I tried debugging and it stops at line 22 (files = matlab.apputil.getInstalledAppInfo;). I assume this is some issue with the way the app is getting installed in 2017a. Do you know about any compatibility issue with new versions of matlab?

MathWorks Learning

karazi amina

Marcus Vollmer

Dear Gang Chen,
Please make sure that you are using a Matlab version of at least R2014b. Please uninstall the toolbox and make sure that the corresponding folder in the application path was completely removed before you install the new version of HRVTool (v0.98). In case of further error please contact me via email.

Best,
Marcus

gang chen

Thank you for your toolbox, but i can't import my data by the GUI.
when i star the GUI, the following mistake message will be display:
error HRVTool (line 500)
F.htoolbar = findall(F.fh,'tag','FigureToolBar');

Marcus Vollmer

Dear Rafael,

please comment the lines 22-24 in HRVTool.m or install the equivalent Matlab-App from http://marcusvollmer.github.io/HRV/

Best
Marcus

Rafael J.

Thanks for posting this toolbox. It looks very powerful. You say it can load waveforms, so can it load in a raw ECG signal?

I try to run the GUI by typing in HRVTool but am receiving the following error:

Index exceeds matrix dimensions.

Error in HRVTool (line 23)
[path,~,~] = fileparts(files(1).location);

I am running this in Matlab 2015b. Thanks in advance.

MATLAB Release Compatibility
Created with R2020b
Compatible with R2016b and later releases
Platform Compatibility
Windows macOS Linux

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