AnyWave:H2

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Purpose

The plugin computes the connectivity between channels using h2/r2 algorithms.
It will produce a .mat file containing the results. This file can be then processed either in MALMAB or by the Correlation Graphs plugin of AnyWave.

How to run

Step 1 - Selected channels of interest:
Before running the plugin, make sure you have selected the channels of interest.
If no channels are selected before running the plugin, you will get a warning message. Computing on many channels can lead to long calculation as many pairs of channels must be considered.
Step 2 - Select data of interest:
Mark the data of interest with one or more markers.
It's a good practice to give the markers an explicit name.
Step 3 - Run the plugin:
There are two ways to run the plugin:

  • Running using the Processes menu of AnyWave.
  • Running from the markers GUI.

Run from the menu

H2Menu.png

Run from markers

LaunchFromMarkers.png

Main GUI

H2GUI.png

Computation parameters:
Change here the computation method (h² or r²) and the timing parameters.

Data input:
- Step 1 (OPTIONAL) : reduce computation time by downsampling the data.
By default the ratio is 1 meaning that no downsampling will be applied.
Change the ratio if you want to reduce computation time.

- Step 2 : skip AND/OR use markers (this section will be hidden if you have launched the the plugin using the markers).

Avoiding artefacted data (OPTIONAL):
Pick a marker name that matches an artefacted region in the data and click the skip button to add it to the main list of markers to avoid.
All the markers with that name will be skipped.
H2skipmarker.png

Using markers:
Pick a marker name that matches data region you want to use and click the Use button to add the name to the main list of markers to use.
H2usemarker.png

In our example we will compute the correlations on all markers named h2 avoiding markers named artefact that may overlapped the h2 markers.

IMPORTANT: If you dont specify markers to use, the plugin will use ALL the markers available (with a duration) and will compute the correlations of the corresponding part of the data.

Frequency bands

You can compute the connectivity on different frequency bands.
By default, the AnyWave band is selected which means the filter options set in AnyWave will be used.
You can enable the different predefined bands and even change the frequency boundaries.

Review resulting graphs

When the computation is finished, the resuslts are saved to a MATLAB file located in the data file's folder.
Another plugin is automatically launched allowing you to browse the different connectivy graphs:
H2graphs ui.png
The UI propose all the graphs resulting from the computation. A graph for each frequency band.
You can see what algorihtm was used on what frequency band and the number of sections which is the number of selected part of data used for computation.

Click on rows to select them and click on View to see the graphs.

Batch mode

The plugin is able to run in batch mode.
See this section for more details

json settings for h2/r2:

{ 
"plugin" : "h2",
"algorithm" : "r2",
"time_window" : 4,
"max_lag" : 0.1,
"step" : 1,
"downsampling_factor" : 2,
"output_prefix" : "my_result"
}

Common options that can also be specified in the command line if you want to apply them to a specific file and not ALL the files:

key description default behavior
marker_file path to the .mrk file to use if not specified, AnyWave will try to locate the .mrk associated with the data file and use it.
use_markers array of marker labels to use optional but may required marker_file option.
skip_markers array of marker labels to SKIP (artefacts) optional but may required marker_file option.
hp high pass filter in Hz optional
lp low pass filter in Hz optional

H2 specific options:

key description requirement default behavior
plugin Name of plugin MANDATORY n/a
time_window the time window in s. MANDATORY n/a
max_lag maximum lag in s. MANDATORY n/a
step step in s. MANDATORY n/a
downsampling_factor downsampling data OPTIONAL default is 1. 2 means the sampling rate of the data will be divided by 2.
output_prefix prefix of resulting file name OPTIONAL default is no prefix.

Example

using this json file:

{ 
"plugin" : "h2",
"algorithm" : "r2",
"time_window" : 4,
"max_lag" : 0.1,
"step" : 1,
"downsampling_factor" : 2,
"output_prefix" : "my_result",
"use_markers" : [ "EI" ]
}

We will compute on a file stored in D:\Data\

anywave --run h2.json --input_file d:\data\data_file.eeg --marker_file d:\data\data_file.mrk --hp 1 --lp 45

This will compute compute r2 values for the file data_file.eeg using 1-45Hz frequency band only on data marked by a EI marker.