AnyWave:H2

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

Run from markers

Main GUI

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 (OPTIONAL) : skip AND/OR use markers (this section will be hidden if you have launched the the plugin using the markers). Avoiding artefacted data:
Pick a marker that matches an artefacted region in the data and click the skip button to add it to the main list of markers to avoid.

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:

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.