MNE-BIDS Command Line Interface (CLI)#

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

mne_bids calibration_to_bids#

Write Elekta/Neuromag/MEGIN fine-calibration data to BIDS.#

Usage: mne_bids calibration_to_bids options args

Options#

--version: show program’s version number and exit
-h, --help: show this help message and exit
--bids_root=BIDS_ROOT: The path of the folder containing the BIDS dataset
--subject_id=SUBJECT: Subject name
--session_id=SESSION: Session name
--file=FNAME: The path of the crosstalk file
--verbose: Whether do generate additional diagnostic output

example usage: $ mne_bids calibration_to_bids –subject_id=01 –session=test –bids_root=bids_root –file=sss_cal.dat

mne_bids count_events#

Count events in BIDS dataset.#

Usage: mne_bids count_events options args

Options#

--version: show program’s version number and exit
-h, --help: show this help message and exit
--bids_root=BIDS_ROOT: The path of the BIDS compatible folder.
--datatype=DATATYPE: The datatype to consider.
--describe: If set print the descriptive statistics (min, max, etc.).
--output=OUTPUT: Path to the CSV file where to store the results.
--overwrite: If set, overwrite an existing output file.
--silent: Whether to print the event counts on the screen.

example usage: $ mne_bids count_events –bids_root bids_root_path

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 crosstalk_to_bids#

Write Elekta/Neuromag/MEGIN crosstalk data to BIDS.#

Usage: mne_bids crosstalk_to_bids options args

Options#

--version: show program’s version number and exit
-h, --help: show this help message and exit
--bids_root=BIDS_ROOT: The path of the folder containing the BIDS dataset
--subject_id=SUBJECT: Subject name
--session_id=SESSION: Session name
--file=FNAME: The path of the crosstalk file
--verbose: Whether do generate additional diagnostic output

example usage: $ mne_bids crosstalk_to_bids –subject_id=01 –session=test –bids_root=bids_root –file=ct_sparse.fif

mne_bids inspect#

Inspect MEG and EEG raw data, and interactively mark channels as bad.#

Usage: mne_bids inspect options args

Options#

--version: show program’s version number and exit
-h, --help: show this help message and exit
--bids_root=BIDS_ROOT: The path of the folder containing the BIDS dataset
--subject_id=SUBJECT: Subject name
--session_id=SESSION: Session name
--task=TASK: Task name
--acq=ACQUISITION: Acquisition parameter
--run=RUN: Run number
--proc=PROCESSING: Processing label.
--rec=RECORDING: Recording name
--type=DATATYPE: Recording data type, e.g. meg, ieeg or eeg
--suffix=SUFFIX: The filename suffix, i.e. the last part before the extension
--ext=EXTENSION: The filename extension, including the leading period, e.g. .fif
--find_flat=FIND_FLAT: Whether to auto-detect flat channels and time segments
--l_freq=L_FREQ: The high-pass filter cutoff frequency
--h_freq=H_FREQ: The low-pass filter cutoff frequency
--verbose: Whether do generate additional diagnostic output

example usage: $ mne_bids inspect –subject_id=01 –task=experiment –session=test –datatype=meg –suffix=meg –bids_root=bids_root

mne_bids mark_channels#

Mark channels in an existing BIDS dataset as “bad”.#

Usage: mne_bids mark_channels options args

Options#

--version: show program’s version number and exit
-h, --help: show this help message and exit
--ch_name=CH_NAMES: The names of the bad channels. If multiple channels are bad, pass the –ch_name parameter multiple times.
--status=STATUS: Status of the channels (Either “good”, or “bad”).
--description=DESCRIPTIONS: Descriptions as to why the channels are bad. Must match the number of bad channels provided. Pass multiple times to supply more than one value in that case.
--bids_root=BIDS_ROOT: The path of the folder containing the BIDS dataset
--subject_id=SUBJECT: Subject name
--session_id=SESSION: Session name
--task=TASK: Task name
--acq=ACQUISITION: Acquisition parameter
--run=RUN: Run number
--proc=PROCESSING: Processing label.
--rec=RECORDING: Recording name
--type=DATATYPE: Recording data type, e.g. meg, ieeg or eeg
--suffix=SUFFIX: The filename suffix, i.e. the last part before the extension
--ext=EXTENSION: The filename extension, including the leading period, e.g. .fif
--verbose: Whether do generate additional diagnostic output

example usage: $ mne_bids mark_channels –ch_name=”MEG 0112” –description=”noisy” –ch_name=”MEG 0131” –description=”flat” –subject_id=01 –task=experiment –session=test –bids_root=bids_root

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=EVENTS: 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)
--line_freq=LINE_FREQ: The frequency of the line noise in Hz (e.g. 50 or 60). If unknown, pass None

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

mne_bids report#

Summarize basic properties of the dataset and write it to stdout.#

Usage: mne_bids report options args

Options#

--version: show program’s version number and exit
-h, --help: show this help message and exit
--bids_root=BIDS_ROOT: The path of the BIDS compatible folder.

example usage: $ mne_bids report –bids_root bids_root_path