cmp.cli.connectomemapper3_singularity module

This module defines the connectomemapper3_singularity script that wraps calls to the Singularity BIDS APP image.

cmp.cli.connectomemapper3_singularity.create_singularity_cmd(args)

Function that creates and returns the BIDS App singularity run command.

Parameters

args (dict) –

Dictionary of parsed input argument in the form:

{
    'bids_dir': "/path/to/bids/dataset/directory",
    'output_dir': "/path/to/output/directory",
    'analysis_level': "participant",
    'participant_label': ['01', '02', '03'],
    'anat_pipeline_config': "/path/to/ref_anatomical_config.json",
    'dwi_pipeline_config': "/path/to/ref_diffusion_config.json",
    'func_pipeline_config': "/path/to/ref_fMRI_config.json",
    ('number_of_threads': 1,)
    ('number_of_participants_processed_in_parallel': 1,)
    ('mrtrix_random_seed': 1234,)
    ('ants_random_seed': 1234,)
    ('ants_number_of_threads': 2,)
    ('fs_license': "/path/to/license.txt",)
    ('notrack': True)
}

Returns

cmd – String containing the command to be run via subprocess.run()

Return type

string

cmp.cli.connectomemapper3_singularity.main()

Main function that creates and executes the BIDS App singularity command.

Returns

exit_code –

An exit code given to sys.exit() that can be:

• ’0’ in case of successful completion

• ’1’ in case of an error

Return type

{0, 1}