The Neurophysiological Biomarker Toolbox (NBT)



Biomarker Computation

Version: 2015

Approximate time needed to complete the tutorial: 15 min.

Once you have cleaned all the data from bad channels, transient artifacts and other physiological artifacts with ICA, you can start computing the biomarkers. The biomarker analysis will be automatically saved in an analysis file with the same name of the original file (e.g. Test.S0001.200100122.ECR5_analysis.mat).

NBT is provided with several biomarkers, such as Amplitudes in classical frequency bands (1-3 Hz, 3-7 Hz, 8-13 Hz, 16-36 Hz, 36-45 Hz), Correlation, Detrended fluctuation Analysis, Coherence, Phase Locking Value, etc. Only few of these biomarkers will be used for this course.

Here, we present the steps for computing Amplitudes of the signal in classical frequency bands, a standard biomarker used in EEG analysis, using the NBT GUI.

  • Open NBT GUI by typing NBT in the command window. If you have NBT GUI already opened go to File|Load NBT Signal and select the file you have just cleaned.
  • Then go to Compute Biomarkers|For Current NBT Signal|Amplitudes. NBT will automatically compute the absolute and normalized Amplitudes for the different frequency bands and save these biomarkers in the analysis files. A message like this will appear in the command window:
Computing Amplitudes for Test.S0001.20100122.ECR5
NBT: Analysis File already exists. Appending to existing file!
NBT: Analysis File already exists. Appending to existing file!
NBT: Analysis File already exists. Appending to existing file!
NBT: Analysis File already exists. Appending to existing file!
NBT: Analysis File already exists. Appending to existing file!
NBT: Analysis File already exists. Appending to existing file!
NBT: Analysis File already exists. Appending to existing file!
NBT: Analysis File already exists. Appending to existing file!
NBT: Analysis File already exists. Appending to existing file!
NBT: Analysis File already exists. Appending to existing file!
  • In order to visualize the computed biomarkers, go to Biomarker statistics | Current Signal, select one of the computed biomarkers (e.g., amplitude_8_13_Hz), then select Channels, select mean, then select CleanedSignalInfo. A figure similar to the one below will appear: the first plot on the left is the interpolated topoplot of the biomarker (you can see how alpha power is higher in the occipital region), the second plot shows the actual values of the amplitude for each channels, the third and the forth plots show the mean value of the biomarker in each region.

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tutorial/biomarker_computation.txt · Last modified: 2015/06/08 22:25 by Klaus Linkenkaer-Hansen
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