MNE-BIDS Command Line Interface (CLI)

Here we list the MNE-BIDS tools that you can use from the command line.

mne_bids cp

Rename files (making a copy) and update their internal pointers.

Usage: mne_bids cp -i INPUT -o OUTPUT

Options

--version

show program’s version number and exit

-h, --help

show this help message and exit

-i INPUT, --input=INPUT

Path to the input file. Accepted formats are BrainVision (.vhdr), EEGLAB (.set), CTF (.ds).

-o OUTPUT, --output=OUTPUT

Path to the output file. MUST be same format as input file.

-v, --verbose

Set logging level to verbose

example usage: $ mne_bids cp –input myfile.vhdr –output sub-01_task-test.vhdr

mne_bids raw_to_bids

Write raw files to BIDS format.

Usage: mne_bids raw_to_bids options args

Options

--version

show program’s version number and exit

-h, --help

show this help message and exit

--subject_id=SUBJECT_ID

The subject name in BIDS compatible format(01,02, etc.)

--task=TASK

Name of the task the data is based on.

--raw=RAW_FNAME

The path to the raw MEG file.

--output_path=OUTPUT_PATH

The path of the BIDS compatible folder.

--session_id=SESSION_ID

The session name in BIDS compatible format.

--run=RUN

The run number for this dataset.

--acq=ACQ

The acquisition parameter.

--events_data=EVENTS_DATA

The events file.

--event_id=eid

The event id dict.

--hpi=HPI

The path to the MEG Marker points

--electrode=ELECTRODE

The path to head-native Digitizer points

--hsp=HSP

The path to headshape points.

--config=CONFIG

The path to the configuration file

--overwrite=OVERWRITE

Boolean. Whether to overwrite existing data

--allow_maxshield

Boolean. Whether to allow non Maxfiltered data.

example usage: $ mne_bids raw_to_bids –subject_id sub01 –task rest –raw data.edf –output_path new_path