The bidsme CLI interface

August 25, 2023 ยท View on GitHub

If the installation of the bidsme was performed using pip (see instructions), then the command line interface bidsme and bidsme-pdb should be available in the terminal. The two interfaces are identical except the second one executes within a standard Python3 debugger pdb.

If bidsme was installed manually, then the same interface can be achieved by calling main.py:main function.

The main interface

usage: bidsme [-h] [-c conf.yaml] [--conf-save] [-v]  subcommand

The main interface bidsme require a sub-command, corresponding to one of the bidsification step:

  • prepare, to prepare dataset
  • process, to process dataset
  • bidsify, to bidsify dataset
  • map, to create bidsmap

For example,

bidsme bidsify <options>

will execute bidsification step.

Some general optional parameter can be passed before the command:

  • -h prints help for main interface
  • -v prints the version of program and version of supported BIDS
  • -c, '--configuration` with path to the configuration yaml file allow to retrieve the saved parameters
  • --conf-save will save current command-line parameters into configuration file

Sub-command interface

All sub-commands will require two positional arguments:

  • source -- path to dataset on which subcommand must be executed
  • destination -- path where the results of the subcommand will be written

For the prepare subcommand, source is the raw dataset and destination will be prepared dataset. For the process subcommand, source and destination is prepared dataset. For all other subcommands the source is prepared dataset, and destination is bidsified dataset.

All subcommands will have common parameters, described below.

Logging options

Logging options, corresponding to the logging section of configuration file:

  • -q, --quiet suppress the standard output, useful for running in the script
  • --level sets the message verbosity of the log output, from very verbose DEBUG, to showing only critical message CRITICAL
  • --formatter sets the log line format message

Plugin options

Plug-in options, corresponding to the plugins section of configuration file. They affect only the relevant commands:

  • --plugin sets the path to the plugin file
  • -o Name=Value sets the options passed to InitEP funcion of the plugin

Subject and session selection options

Subject and session selection, corresponding to the selection section of the configuration file

  • --participants corresponds to the space separated list of participants to process. Listed participants are retrieved after the bidsification, with sub- prefix
  • --skip-in-tsv is a switch that allows to skip participants, if already present in the specified destination
  • --skip-existing is a switch that allows to skip participants, if a corresponding folder already exists in the specified destination
  • --skip-existing-sessions is a switch that allows to skip participants, if a corresponding session already exists in the specificied destination

General options

General options, non existing in configuration file:

  • --dry-run, allows to run commands in simulation mode, without writing any outputs outside of the logs. The non-writing is not garanteed in the plugins, user must ensure himself that nothing is written in plugin in dry mode.

The full list of commands parameters can be seen using the -h option: bidsme.py [command] -h.