Command reference

This section lists every neuroatlas command and its options, one page per group of commands. Run neuroatlas <command> --help to see the same text in the terminal. The user guide shows how the commands fit together.

Global options

These options work with every command, before or after the command name.

Usage: neuroatlas [-v] [--log FILE] [--online] <command> [options]

Option	Description
-v, --verbose	Show more detail, library log lines and full tracebacks.
--log FILE	Also write all output, log lines and tracebacks to FILE.
--online	Allow downloads. Only the commands that download are online by default.
-V, --version	Print the version, and the commit when run from a git clone.

Every command exits with status 0 when it succeeds, 1 when a run fails and 2 when the command line is wrong.

Commands

Group	Command	Description
Setup	config	Set where data, caches, results and model weights are stored.
Explore	list	List the benchmarks, datasets, models, aliases or tasks.
	show	Describe a benchmark and print the commands it runs.
Data and weights	data	Check, download and prepare datasets.
	models	Check and download model weights.
Run	check	Test each dataset and model on one batch before a long run.
	run	Run a benchmark on this machine.
	submit	Write HTCondor or SLURM jobs for a benchmark.
	status	Show the state of the jobs that submit wrote.
Results	results	Summarise a benchmark's results.
	rescore	Recompute the metrics from saved test predictions.
Individual steps	embed	Extract embeddings of one dataset with frozen models.
	probe	Fit probes on extracted embeddings.
	hypnogram	Compute hypnograms and sleep features from sleep staging results.