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_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)
- --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¶
Write raw files to BIDS format.¶
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