Simple CLI for importing EEG data to BIDS format.
Clone the repo and run pip install on the root directory.
usage: import-bids [-h] [--eog EOG CONFIG FILE] [--ref EOG CONFIG FILE]
[-m MONTAGE NAME | -t MONTAGE PATH | -d MONTAGE DIRECTORY | -l ELEC PATH] [-c CHANNEL NAME PATH]
[-a | -s CHANNEL NAME] [-e EVENT ID PATH] [-M METADATA PATH] [-f LINE FREQUENCY] [-v] [-vv]
[--dry-run] [-o] [-P] [-n N CPUS]
raw_dir bids_dir task
Tool to import EEG files to the BIDS data format.
positional arguments:
raw_dir Directory containing the raw data
bids_dir Output directory for the BIDS dataset
task Task name in the run.
optional arguments:
-h, --help show this help message and exit
--eog EOG CONFIG FILE
Path to EOG configuration file
--ref EOG CONFIG FILE
Path to reference configuration file
-m MONTAGE NAME, --montage MONTAGE NAME
Name of standard montage to use. Template will be loaded from MNE.
-t MONTAGE PATH, --template MONTAGE PATH
Path to template file to load.
-d MONTAGE DIRECTORY, --dig_dir MONTAGE DIRECTORY
Directory for subject digitization files.
-l ELEC PATH, --location ELEC PATH
FieldTrip .elec file specifying electrode positions.
-c CHANNEL NAME PATH, --channel_names CHANNEL NAME PATH
Path to file containing mapping between channel names and standard 1020 names.
-a, --annotations Get event times from annotations.
-s CHANNEL NAME, --stim CHANNEL NAME
Get events from stimulus channel.
-e EVENT ID PATH, --event_id EVENT ID PATH
Get event names from file mapping trigger values to event names. Must be a .tsv file with
trigger number in first column and event name in the second column.
-M METADATA PATH, --metadata METADATA PATH
Path to metadata file. Must be a .tsv file with length equal to the number of events and the
subject id in the first column.
-f LINE FREQUENCY, --line_freq LINE FREQUENCY
Line frequency for powerline noise. Defaults to 50.0 Hz.
-v, --verbose Verbose output. Equivalent to MNE log-level 'INFO'.
-vv, --debug Debug output. Equivalent to MNE log-level 'DEBUG'.
--dry-run Do not save the results
-o, --overwrite Overwrite existing files.
-P, --progress No not display progressbar.
-n N CPUS, --n_parallel N CPUS
Number of parallel processes. Defaults to 1.