AnyWave:ICA

ICA Plug-in

This plugin will extract Independent Components from signals.
The algorithm used is the Infomax algorithm.
This plug-in will run in the background, doing the computation and then a file will be created containing the resulting matrices: (mixing and unmixing matrices).
The only user interface is the one which let the user set all the settings before the computation is done.

Algorithm

The plug-in was designed to implement several algorithms but only infomax is implemented so far.

Filtering

The user can specify a frequency bandwidth to use by defining a low pass and a high pass filtering.
Note that decimation will be applied depending on the low pass filtering, to shorten the calculation time and minimize the memory usage.

Data Input

The user must choose on what type of signal the computation will be done (EEG or MEG).
By default, bad channels are excluded. Finally, markers can be used to remove bad part of the signals (artifacts, etc.), the user must first add markers by itself or using another plug-in with an explicit name.

Data Output

The number of components is by default limited to 50 but all the components can be extracted at the cost of a longer calculation.
By default, a result file will be created in the data folder. This file can be imported afterward in AnyWave by using the Load ICA Components feature.

Batch mode

This plugin can run in command line or batch mode.
Here are the recognized command line arguments:

ICA arguments

key	description	requirement	default behavior
plugin	Name of plugin	MANDATORY	this is a required key when using a json file. Not applicable without a json file.
modality	channel modality (MEG, EEG, ...)	MANDATORY	n/a
downsampling	enable/disable downsampling of data	OPTIONAL	default is true
comp	number of expected components (PCA applied if comp < n channels)	OPTIONAL	if not specified, comp will be the number of channels of the modality.
skip_bad	true if ignoring bad channels	OPTIONAL	default is true

Common arguments

key	description	requirement	default behavior
input_file	file to process	MANDATORY	n/a
output_dir	output directory full path	OPTIONAL	default is to output in data file's directory.
output_file	filename to generate	OPTIONAL	default is to create a filename based on data file name and add suffixes to it.
ouput_prefix	prefix the name of the output file (useful for BIDS operation)	OPTIONAL	No prefix set as default.
hp	high pass filter	OPTIONAL	is not specified operates on raw data.
lp	low pass filter	OPTIONAL	is not specified operates on raw data.

Examples

Using a json file to call the plugin:

{
"plugin": "ica", 
"comp" : 50,
"downsampling" : false,
"modality" : "MEG",
"use_markers" : [ "selection1", "selection2"],
"skip_markers" : [ "artefact", "artefacted" ]
}

anywave --run ica.json --hp 1 --lp 70 --input_file /path_to_file/myfile.dat

Not using json file:

anywave --run ica --modality MEG --comp 50 --downsampling false --hp 1 --lp 70 --input_file /path_to_file/myfile.dat --skip_bad false