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Command-Line Interface

After installation, the meegflow command is available on your PATH.

Synopsis

meegflow --bids-root PATH --config PATH [OPTIONS]

Options

Option Type Description
--bids-root path Root directory of the BIDS dataset (required)
--config path Path to the YAML pipeline configuration file (required)
--subjects list Subject ID(s) to process (default: all)
--sessions list Session ID(s) to process (default: all)
--tasks list Task name(s) to process (default: all)
--acquisitions list Acquisition label(s) to process (default: all)
--runs list Run number(s) to process (default: all)
--extension str File extension filter (default: .fif when the datatype is meg, .vhdr otherwise)
--datatype str BIDS datatype to process: eeg, meg, ieeg or nirs (BIDS reader only; defaults to the config's top-level datatype, otherwise detected from the dataset)
--log-file path Write MNE log to this file (appended)
--log-level str MNE log level (DEBUG, INFO, WARNING, …). Default INFO

Examples

Process all subjects

meegflow \
    --bids-root /data/my_study \
    --config config.yaml

Process specific subjects and tasks

meegflow \
    --bids-root /data/my_study \
    --config config.yaml \
    --subjects 01 02 03 \
    --tasks rest

Save log to file

meegflow \
    --bids-root /data/my_study \
    --config config.yaml \
    --log-file logs/preproc.log \
    --log-level DEBUG