Command Line Interface

With the command linea interface you can run a configuration file from the command line, e.g.:

$ brain_pipe config_file.extension # e.g. typical_processing.yaml

See also Defining and running Pipelines through configuration files for more information on how to write a configuration file.

API

usage: [-h] [--parser PARSER] [--parser_files PARSER_FILES]
                   input_file

Preprocess brain imaging data

positional arguments:
  input_file            Input file containing the pipeline definitions.

options:
  -h, --help            show this help message and exit
  --parser PARSER       Name of the parser to use when processing the input
                        file. If not specified, the parser will be determined
                        based on the file extension.
  --parser_files PARSER_FILES, -f PARSER_FILES
                        Path to external file containing the parser to use
                        when processing the input file. Only necessary when
                        defining your own parser. When multiple files are
                        provided, the first parser found will be used. 'None'
                        or '*' can be used to search the files in the
                        brain_pipe package. Default is all files in the
                        brain_pipe package.