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: 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

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

--task=TASK

name of the task the data is based on

--raw=RAW_FNAME

path to the raw MEG file

--bids_root=BIDS_ROOT

The path of the BIDS compatible folder.

--session_id=SESSION_ID

session name in BIDS compatible format

--run=RUN

run number for this dataset

--acq=ACQ

acquisition parameter for this dataset

--events_data=EVENTS_DATA

events file (events.tsv)

--event_id=eid

event id dict

--hpi=HPI

path to the MEG marker points

--electrode=ELECTRODE

path to head-native digitizer points

--hsp=HSP

path to headshape points

--config=CONFIG

path to the configuration file

--overwrite=OVERWRITE

whether to overwrite existing data (BOOLEAN)

--allow_maxshield

whether to allow non maxfiltered data (BOOLEAN)

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