Download this pdf manual for instructions on how to save and retrieve both Excel/asc2 data and IBI signals converted for Kubios analysis:
KUBIOS ANALYSIS FOR HRV RESEARCH APPLICATIONS:
PhysioPilot's signals are truly research-grade. In our project consultations we have listened to the needs of our researchers, and designed two simple ways to record and save data in formats that are easily opened by leading data management programs:
1. Excel-based Time Series: For general signal analysis, data is imported in Excel and asc2 formats, allowing a large variety of spreadsheet and database-structured statistical programs to use the data.
2. Kubios Event-based Series: This applies only to the IBI data. A special conversion is needed to convert IBI data for use in the widely-used free Kubios HRV Analysis program.
PhysioData provided both kinds of formats, for maximum flexibility.This Webpage highlights Kubios Analysis.
Link to the download registration site for the latest Kubios HRV Analysis software.
Download PhysioData Guide to Kubios Analysis of Saved IBI Data - June 2009. [pdf format]
Register here: Kubios HRV Analysis Software
STEP-BY-STEP TROUBLESHOOTING GUIDE
Courtesy of > Christina Huang
> Clinical Psychology Doctoral Student
> California School of Professional Psychology
> Alliant International University
> phone: 512.731.7399
>NOTE: THIS IS FROM AN ONGOING DISCUSSION. SHE IS NOT PART OF THE COMPANY AND IS A STUDENT:
"> 1. If you go to your J&J software start screen, you should see a button that says "Manage Data."
> 2. Select the appropriate client and then select "Export."
> 3. Another window will pop up. On the top left, click on “HR/IBI” and make sure to double check where your file will be saved by clicking on the drop down menu. J&J usually saves files in some hidden folder like your computer's program files, so you may want to create a new folder on the desktop or somewhere that is easier for you to find to save your data in.
> 4. Double check all the signals that will be exported in the bottom right hand side of the window.
> 5. Click ok. Your data should be exported in IBI format to the file you have chosen to save it in. Now you should be able to physically open it and look at the data. You have 2 options here. You can either open it in Excel, in which you could add an extra column for time, or you can open it in Notepad (which is what I usually do) by right-clicking and manually choosing the program to open your data with. When you go back to Kubios, just choose the same file in the "Open File" tab on the toolbar and Kubios should be able to open it as well. As long as your data is in IBI format, Kubios can open it regardless of whether you saved it in Excel or Notepad.
>
> Try this to see if you can physically look at your data in IBI format...Files that Kubios can't open are usually because a 0 is contained in the IBI data. ...This list of numbers is where you should find 0s. To answer your question about the data having been recorded in the same manner - it doesn't matter here because ectopic beats or irregular heart rhythms are more likely to appear when a person is in the stressor phase for example.
>;;;
>
> Christina Huang
> Clinical Psychology Doctoral Student
> California School of Professional Psychology
> Alliant International University
> phone: 512.731.7399"
chuang3@alliant.edu
RESEARCH APPLICATIONS USING HRV or ECG
Protocol for Exporting J&J Data
1. After recording your session, exit out of J&J.
2. A small window will pop up in the middle of the screen asking you to select and name a client.
3. Click "Save to Database" and then "Export."
4. A new window will pop up. On the top left, click on "HR/IBI" and make sure to double check where your file will be saved by clicking on the drop down menu. Also double check all the signals that will be exported in the bottom right hand side of the window.
5. Click ok. Your data should be exported in IBI format to the file you have chosen to save it in.
Protocol for HRV Biofeedback manual cleanup using Kubios HRV
1. Open Kubios HRV software, then open your data through this program in the File dropdown menu.
2. At the same time, open up the actual notepad or excel file that you are cleaning and position the window next to the Finnish program.
3. When you ve opened the file in the Finnish program, it will show you what it actually looks like on the top right hand portion of the screen in the form of a graph with Time as the X-axis and RR(s) as the Y-axis. Each data point (blue dots in the picture) corresponds to each # in the Notepad or excel file and represents one second of data. The picture will help you to be able to see visually which data points might be ectopic. If the graph looks too hectic and you have trouble being able to see any trends, you can extend the range. There is a box directly under the graph to the very right labeled "Range(s)." To spread out the data, manually type in a smaller # here.
4. To the left hand side of the screen approximately in the middle, there is a box labeled "Remove trend components." In the Methods dropdown menu, change the option from "None" to "Smoothn Priors." This will add a curve to the graph by averaging out the center of the data points.
5. Unfortunately, the criteria for deciding what data points to clean is arbitrary. You just have to eyeball the data and see which data points look abnormal and which represent actual significant trends. For example, if the data points gradually go up, then you probably won t need to delete any, but if there is a small cluster of data points that are far removed from everything else that do not appear to be part of a trend, it would be best to delete them. Remember, it s better to average out any points that might be ectopic than to leave them as is. Methodologically, it s probably a good idea to note which sets of data you have removed and to offer an explanation via your observations during the recording session. Ectopic beats can be caused by anything, such as the participant laughing, coughing, moving their hand, changing seating position, etc…
If your data has specific subsections in it (i.e. baseline, paced, stressor, recovery, etc…) and you want to examine each section separately but have not already manually separated them into discrete files, you can manipulate the graph by extending or narrowing the highlighted region to reflect the length of time of these segments. Double click on the graph until a compass appears, then drag the edge of the highlighted portion to correspond with the time segments you have. For example, if you are only interested in examining the paced breathing section which occurs from minutes 5-8, drag the highlighted portion to highlight only these minutes.
The statistics in the report will give you numbers calculated based off the highlighted regions only.
6. Using the picture to gauge which points you ll need to delete, find these same beats in the notepad or excel file. This step is extremely tedious and the data point may be difficult to find. If you have trouble finding it, you can either use the seconds on the x-axis of the picture in the Finnish program or look at the #s in the file. For example, in the notepad or excel file, if all of the #s are in the 600 range and then you all of a sudden see a # that is 750, it s probably the one you want to delete. Remember again, each of the data points you see in the Kubios graph represents each of the #s you have in IBI format and correspond by time as well, so if you are specifically looking at an ectopic beat that occurs at the 1 minute marker in Kubios, you can scroll 60 #s down in your data file to find that #.
7. Once you ve found the data point you want to take out, go to the notepad/excel file and delete it. Replace it with the average of the 2 #s on either side of it, or in other words, the average of the #s directly preceding and following it.
8. Each time you ve done this, resave the notepad or excel file and reopen it using the Finnish software to see what the new file looks like. This way, you can keep track of the changes you ve made and not have to repeat any of your work in case something happens.
9. Continue to do this for each and every single file.
10. When you put the data into SPSS, go to the toolbar of the Finnish program and go to "report sheet" under "View" in the top left hand corner.
11. In the Report, look at the left column of data that s labeled "Time Domain Results." Under "Statistical Measures," you ll see:
-Mean RR*
-STD RR (SDNN)
-Mean HR*
-STD HR
-RMSSD
-NN50
-pNN50
-RR Triangular Index
-TINN
You want to take note of everything but STD of mean HR and NN50 (underlined above).
12. In the bottom left column you ll see "Frequency Domain Results" that are faintly highlighted blue. Of the 4 columns (peak; power: ms2; power: %; power: n.u.), take notes of the last 2 power columns (% and n.u.) for all bands: VLF, LF, HF, and LF/HF.
13. Still in the Frequency Domain on the right column, you ll see the parametric spectrum labeled AR Spectrum for Auto-Regressive Peak. Take note of the highest first peak in this graph and its PSD value.
14. Under the Nonlinear Results at the bottom of the report, take note of the SD1 and SD2 under the "Poincare Plot" as well as the Approximate Entropy (ApEn) under the "Other" table. The Approximate Entropy tells you how regular the signal is.
*Each of these measures will be a separate column in SPSS.
The application was [2b][[2EMG] +ECG +T+SC+Resp]@1024cps.is found under the I-330-C2 PLUS 12 ch Hardware Type but it may work with a C2 Plus 6 ch.
Note in the instructions the steps to follow when using a 6 ch.
DATA TYPES:
KUBIOUS and IBIs: Export data from the IBI table quickly with Kubios.
EXCEL and ECGs: You can export the ECG table. It will take a long time to generate just 3 min of data in the excel file.
QRS Tools and Excel ECGs: Convert the excel ECG file into a text file and import the file into QRS Tools.
Steve Porges software: Go over the ECG text file and make sure the R values are correct, then process.
Thanks again Bob, I'll then work on this application to use it in our research project.
Jose
