physiozoo / mhrv

Matlab toolbox for calculating Heart-Rate Variability metrics on ECG signals

PhysioZoo

PhysioZoo is a collaborative platform dedicated to the study of the heart rate variability (HRV) from Humans and other mammals’ electrophysiological recordings. The main components of the platform are:

• Software
  • An open-source algorithmic toolbox for matlab (mhrv), which implements all standard HRV analysis algorithms, a selection of peak detection algorithms and prefiltering routines. This can be used within your own data analysis code using the mhrv API.
  • An open-source graphical user interface (PZ-UI) that provides a user friendly interface for advanced HRV analysis of RR-intervals time series and data visualization tools. This enables easy access to HRV analysis without writing any code.
• Databases
  • A set of annotated databases (PZ-DB) of electrophysiological signals from different mammals (dog, rabbit and mouse). Available here.
  • Manually audited peak locations and signal quality annotations for each of the recordings.
• Configuration
  • A set of configuration files that adapt the HRV measures and mhrv algorithms to work with data from different mammals.
  • All HRV measures can be further adapted for the analysis of other mammals by creating simple human-readable mammal-specific configuration files.

The PhysioZoo mission is to standardize and enable the reproducibility of HRV analysis in mammals’ electrophysiological data. This is achieved through its open source code, freely available user interface and open access databases. It also aims to encourage the scientific community to contribute their electrophysiological databases and novel HRV algorithms/analysis tools for advancing the research in the field.

Feedback on how to improve the PhysioZoo platform is welcomed. Do not hesitate to drop us an email at:

[email protected]

Source code, data or interface enhancement contributions are welcome. Look here on how to contribute to PhysioZoo.

Please include the standard citation to PhysioZoo when using the resources available on the platform:

Joachim A. Behar*, Aviv A. Rosenberg*, Ido Weiser-Bitoun, Ori Shemla, Alexandra Alexandrovich, Evgene Konyukhov, Yael Yaniv. 2018. 'PhysioZoo: a novel open access platform for heart rate variability analysis of mammalian electrocardiographic data.' Accepted for publication in Frontiers in Physiology.

*Equal contribution.

mhrv's Issues

Could not find the wfdb tool 'gqrs.exe'

Hello
An error occurred recently when I run your program.Can you answer it if you have time?
best wishes！

Questions are as follows：

mhrv.mhrv('db/mitdb/111', 'window_minutes', 15, 'plot', true);
[0.016] >> mhrv: Processing record db/mitdb/111 (ch. 1)...
[0.016] >> mhrv: Signal duration: 00:30:05.555 [HH:mm:ss.ms]
[0.016] >> mhrv: Analyzing window 1 of 2...
[0.016] >> mhrv: [1/2] Detecting RR intervals from ECG...
[0.047] >> mhrv: ERROR Analyzing window 1 of 2 in record db/mitdb/111:
Could not find the wfdb tool 'gqrs.exe'. Searched in: E:\matlab project\temp;............

about rectify code and data

Hello, thank you for taking the time to respond. Wishing you smooth work and everlasting happiness in your family!
My ECG data file is in txt format, approximately like this: Each data point is spaced 1ms apart
0 0 0 0 0 270 455 952
1 0 0 0 0 270 454 952
2 0 0 0 0 270 454 952
3 0 0 0 0 270 457 952
4 0 0 0 0 270 462 952
5 0 0 0 0 270 469 952
6 0 0 0 0 270 478 952
7 0 0 0 0 270 489 952
8 0 0 0 0 270 501 952
9 0 0 0 0 270 515 952
10 0 0 0 0 270 529 952
11 0 0 0 0 270 545 952
12 0 0 0 0 270 562 952
13 0 0 0 0 270 580 952
14 0 0 0 0 270 598 952
15 0 0 0 0 270 616 952
0 0 0 0 0 270 632 952
1 0 0 0 0 270 646 952
2 0 0 0 0 270 658 952
3 0 0 0 0 270 668 952
I'm having trouble reading my data with MATLAB because your sample data is in "dat" format. How should I modify my data?

Matrix dimensions must be consistent

Hello
An error occurred recently when I ran your program.The matrix dimensions are inconsistent. Can you answer it if you have time?
best wishes！

Questions are as follows：

mhrv('db/mitdb/111', 'window_minutes', 15, 'plot', true);
[0.016] >> mhrv: Processing record db/mitdb/111 (ch. 1)...
[0.016] >> mhrv: Signal duration: 00:30:05.555 [HH:mm:ss.ms]
[0.047] >> mhrv: Analyzing window 1 of 2...
[0.047] >> mhrv: [1/2] Detecting RR intervals from ECG... 1046 intervals detected.
[0.422] >> mhrv: [1/2] Removing ectopic intervals... 13 intervals removed.
[0.438] >> mhrv: [1/2] Calculating time-domain metrics...
[0.469] >> mhrv: [1/2] Calculating frequency-domain metrics...
[0.656] >> mhrv: [1/2] Calculating nonlinear metrics...

[0.750] >> mhrv: ERROR Analyzing window 1 of 2 in record db/mitdb/111:
The matrix dimensions must be consistent.

Can you give an example of how to use rhrv_batch?

It would be much appreciated. Just use the mitdb example just like in the rhrv call.

run mhrv_init

when i run mhrv_init.m,Failed to download: zip 文件 "C:\Users\Administrator\Desktop\mhrv-master\mhrv-master\bin\wfdb-10.5.24-mingw64.zip",How can I solve this problem?thanks.

unrecognized argument

Hello
An error occurred recently when I run your program.Can you answer it if you have time?

Questions are as follows：

mhrv.mhrv('db/mitdb/111', 'window_minutes', 15, 'plot', true);
[0.078] >> mhrv: Processing record db/mitdb/111 (ch. 1)...
[0.094] >> mhrv: Signal duration: 00:30:05.555 [HH:mm:ss.ms]
[0.141] >> mhrv: Analyzing window 1 of 2...
[0.141] >> mhrv: [1/2] Detecting RR intervals from ECG...
[0.312] >> mhrv: ERROR Analyzing window 1 of 2 in record db/mitdb/111:
gqrs error: program: unrecognized argument Files\MATLAB\R2022a\toolbox\mhrv-master\bin\wfdb\bin\gqrs.exe

skipping window...
[0.312] >> mhrv: Analyzing window 2 of 2...
[0.312] >> mhrv: [2/2] Detecting RR intervals from ECG...
[0.406] >> mhrv: ERROR Analyzing window 2 of 2 in record db/mitdb/111:
gqrs error: program: unrecognized argument Files\MATLAB\R2022a\toolbox\mhrv-master\bin\wfdb\bin\gqrs.exe

skipping window...
[0.406] >> mhrv: ERROR: All windows failed analysis. Exiting...

how can I fix the problem?

RUN .CSV FILE

HI, I have a .csv ECG file, is it possible to run it in your program to extract the HRV features?

Thank u very much!!