CLI Reference#

All functionality is accessed through the lc command, which has several subcommands. Run lc --help or lc <subcommand> --help for inline help.

Global options#

-q, --quiet#

Enable quiet mode. Log level is set to CRITICAL; only fatal errors are printed.

lc prepare#

Set up the analysis directory structure and generate launch scripts.

lc prepare -lcc <config> -ssl <subseslist> [-cc <container_config>]
-lcc, --lc_config <path>#

Path to the main lc_config.yaml file.

-ssl, --sub_ses_list <path>#

Path to the subseslist.tsv file listing subjects and sessions to process.

-cc, --container_specific_config <path>#

Path to the container-specific JSON config file (e.g. rtppreproc.json). Required for container-based pipelines; not needed for analysis-based pipelines (glm, prf).

What it does:

  1. Reads and validates all input configs.

  2. Checks that required input files exist for each subject/session.

  3. Creates the analysis directory under BIDS/derivatives/.

  4. Writes frozen copies of all configs to analysis-dir/config/.

  5. Generates per-subject launch scripts in analysis-dir/scripts/.

  6. Prints a Rich summary table (ready / fixed / warn / blocked per subject).

lc run#

Submit the prepared launch scripts to the HPC scheduler.

lc run -w <workdir> [--run_lc]
-w, --workdir <path>#

Path to the prepared analysis directory (the one created by lc prepare).

-R, --run_lc#

Actually submit jobs. Without this flag, lc run performs a dry run and only prints the commands that would be executed.

lc qc#

Validate outputs after jobs have finished.

lc qc -w <workdir>
-w, --workdir <path>#

Path to the analysis directory to check.

What it produces:

  • A pass/fail summary table printed to the terminal.

  • analysis-dir/logs/qc_TIMESTAMP.log with details of any missing files.

  • analysis-dir/failed_subseslist.tsv listing all subject/sessions that failed, ready to be passed back to lc prepare.

lc copy_configs#

Copy the bundled example config files to a working directory.

lc copy_configs -o <output_path>
-o, --output <path>#

Destination directory. Typically basedir/code/.

lc gen_subses#

Generate a subseslist.tsv from an existing directory tree.

lc gen_subses -b <basedir> -n <filename> [-o <output_dir>]
-b, --basedir <path>#

Directory containing sub-* / ses-* folders to scan.

-n, --name <filename>#

Output filename for the generated subseslist (e.g. subseslist.tsv).

-o, --output_dir <path>#

Directory in which to write the file. Defaults to basedir.

lc create_bids#

Create a minimal fake BIDS directory structure for testing.

lc create_bids -cbc <config> -ssl <subseslist>
-cbc, --creat_bids_config <path>#

Path to the create_bids config YAML file.

-ssl, --sub_ses_list <path>#

Path to the subseslist to use when generating the fake structure.

lc zip_configs#

Archive the current example configs back into the repo (developer utility).

lc zip_configs