Utility Commands

neuromaestro detect-subjects¶

Scans a directory for subject folders matching the given prefix.

# Print detected subjects to stdout
neuromaestro detect-subjects /data/BIDS

# Save to a text file (comma-separated, one line)
neuromaestro detect-subjects /data/BIDS --output subjects.txt

# With explicit prefix (default is "sub-")
neuromaestro detect-subjects /data/raw --prefix "sub-" -o subjects.txt

The saved file can be passed directly to --subjects in neuromaestro run:

neuromaestro run --subjects subjects.txt ...

Arguments / Options:

neuromaestro init¶

Initialises a new project directory with config and script templates copied from the package defaults.

neuromaestro init /scratch/my_study

Creates the following layout under the given directory:

/scratch/my_study/
├── config/
│   ├── config.yaml
│   ├── hpc_config.yaml
│   ├── project_config/
│   └── results_check/
└── scripts/
    └── (template .sh scripts)

Pass --config-dir /scratch/my_study/config in all subsequent neuromaestro commands, or set $NEUROMAESTRO_CONFIG_DIR once to skip it (see Getting Started).

Arguments / Options:

neuromaestro list-tasks¶

Lists every task in config.yaml with its scripts and its input_from task (where its $INPUT_DIR comes from when both run together). Job dependencies are not listed: they follow the DAG rules in Pipeline Tasks Reference.

neuromaestro list-tasks --config-dir /data/config

Options:

neuromaestro-gui¶

Launches the web dashboard.

neuromaestro-gui                 # default port 8050
neuromaestro-gui --port 8051     # if 8050 is in use

On startup it prints a link with a token made for that launch, such as http://127.0.0.1:8050/?token=.... Open that link: the GUI rejects requests without the token, so other users on a shared login node cannot use it. The server listens on 127.0.0.1 only, unless --host 0.0.0.0 is given.

Options:

The GUI has three tabs:

neuromaestro generate-config¶

Generate a blank project config template ({project}_config.yaml). Equivalent to clicking Generate Template in the GUI Project Config tab.

neuromaestro generate-config branch --config-dir /data/config

# Write to a custom directory
neuromaestro generate-config branch --config-dir /data/config \
  --output-dir /scratch/my_project/config/project_config

Arguments / Options:

The command refuses to overwrite an existing {project}_config.yaml and exits with code 1, so regenerating a template cannot silently discard settings you have already filled in. Pass --force when you really do want to start over.

The generated file is a plain YAML skeleton without comments: every key is present with an empty or example value. Open it in the GUI editor or any text editor and fill in paths, modules, and task parameters. See Project Configuration for what each key means.

neuromaestro generate-checks¶

Generate a blank results-check config template ({project}_checks.yaml). Equivalent to clicking New in the GUI Results Check Config tab.

neuromaestro generate-checks branch --config-dir /data/config

# Write to a custom directory
neuromaestro generate-checks branch --config-dir /data/config \
  --output-dir /scratch/my_project/config/results_check

Arguments / Options:

As with generate-config, an existing {project}_checks.yaml is never overwritten unless --force is given.

The generated file contains two example entries, one per block type: rest_preprocess with a required_files check and recon with a count_check. They are active YAML, not comments, so check-outputs and --resume use them as soon as the file exists. Edit or delete them to match your outputs. See Output Checks Configuration for the full reference.