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 (e.g. .vhdr)
--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 configs/config_example.yaml

Process specific subjects and tasks

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

Save log to file

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