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Command Line Operations
convert a file to BIDS Run a plugin

AnyWave allows the user to process data using the command line.
Passing arguments to anywave can be done using the double dash syntax:

anywave --arg1 <value> --arg2 <value> --arg3

An argument may have a value.
There is a list of common arguments that can be used anytime for every command line operation:
--input_file <file> set the file to process.
--input_dir <dir> sets the input directory to use.
--marker_file <file> sets the marker file (.mrk) to use. (path must be absolute)
--montage_file <file> sets the montage file (.mtg) to use. (path must be absolute)
--input_dir <dir> sets the input directory to use.
--output_dir <dir> sets the output directory. The location where the plugin should generate its results.
--output_file <file> sets the name of the processing output file.
--output_prefix <string> sets the prefix of the output file.
--hp <value> sets the high pass filter value to use.
--lp <value> sets the low pass filter value to use.
--notch <value> sets the notch filter value to use.
--skip_bad_chanels <true|false|yes|no> default is true. Set it false to force anywave to also add bad channels to processing input.
--create_montage <bipolar_ieeg|none> create a montage from data file and use it as input for processing. bipolar_ieeg means seeg alike bipolar. none will force AnyWave to ignore .mtg file that may be present along with the data file.
--use_markers "markers" specify the markers to use for processing. sets --use_markers all_data to force AnyWave to use a global marker for the whole data as input.
--skip_markers "markers" specify the markers to avoid while processing. Can be used with use_markers. if --use_markers all_data is set, this option is ignored.

--log_dir <directory> set the output log directory. Every log files generated by the command line will be placed in that directory. The directory must exist.
--run <plugin name> start processing data using a plugin. This will required to specify plugin related options.

Running h² computation on a seeg data file:

anywave --run h2 --time_window 4 --step 1 --max_lag 0.1 --hp 1 --lp 45 --input_file d:\data\seeg\data.vhdr