Revision as of 09:54, 10 April 2020

This is a way to run AnyWave in non GUI mode to process files.

Operations

What can AnyWave do in a command line?

Convert Files to BIDS

AnyWave is used by some third party softwares to process eeg/ieeg/meg files and convert them to BIDS format.
Here is the complete list of options to use to do so:
--toBIDS indicates we want to convert a file to BIDS.
--bids_modality <ieeg|eeg|meg> defines the data modality.REQUIRED
--bids_sub <subject> sets the BIDS subject REQUIRED
--bids_task <task> sets the BIDS task REQUIRED
--bids_ses <session> sets the BIDS session (optional)
--bids_run <run> sets the BIDS run index (optional)
--bids_acq <acq> sets the BIDS acquisition (optional)
--bids_proc <proc> sets the processing applied to the file. (optional)
--bids_output <sidecars|all> defines what output files will be generated (sidecars : only generates .json and .tsv files. all: full conversion)
--bids_format <edf | vhdr> this implies the bids_modaliy was set to eeg or ieeg. Specifies the output file format. Default is vhdr. (optional)

Examples

Convert a file data.eeg containing SEEG recordings to BIDS for subject JohnDoe.

anywave --toBIDS --bids_modality ieeg --input_file d:\data\data.eeg --output_dir d:\data\BIDS --bids_sub johndoe --bids_task rest

Convert a MEG data file (4DNI) to BIDS for subject JohnDoe.
The run number must be specified. Note also that the input is the folder containing the MEG run, not a single file.

anywave --toBIDS --bids_modality meg --input_dir d:\data\MEG\run1 --output_dir d:\data\BIDS --bids_sub johndoe --bids_task rest --bids_run 01

Convert a MEG data file (Elekta) to BIDS for subject JohnDoe.
As everything is stored in one file (.fif), no need here to specify a run number (but you can).
However, the input is still a folder, so specifiy the folder in which the fif file is located.

anywave --toBIDS --bids_modality meg --input_dir d:\data\MEG --output_dir d:\data\BIDS --bids_sub johndoe --bids_task rest

Process files

AnyWave can also process data files, running a specific process (plug-in) to a bunch a files or directories.
The keyword to do that kind of opteration is :
--run
Of course, to run a plugin, the user must set all the required parameters aswell as input and output options.
Input data must and output options may be specified besides setting the process parameters.
There are a list of common command line keywords that can be used anytime:
--